ALS-6411: Null pointer when joining empty patient masks in GenomicPro…

…cessorPatientMergingParentImpl (#107) * ALS-6408: Cleanup bdc genomic config
hms-dbmi · May 8, 2024 · 98ff360 · 98ff360
1 parent 8f6305f
commit 98ff360
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diff --git a/...u/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImpl.java b/...u/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImpl.java
@@ -79,7 +79,8 @@ public Mono<VariantMask> getPatientMask(DistributableQuery distributableQuery) {
     /** A little bit of a hack for now since the masks don't have sizes at this point and they are needed to merge
      */
     public SizedVariantMask appendMask(SizedVariantMask mask1, SizedVariantMask mask2) {
-        return new SizedVariantMask(VariableVariantMasks.appendMask(mask1.variantMask, mask2.variantMask, mask1.size, mask2.size), mask1.size + mask2.size);
+        VariantMask variantMask = VariableVariantMasks.appendMask(mask1.variantMask, mask2.variantMask, mask1.size, mask2.size);
+        return new SizedVariantMask(variantMask != null ? variantMask : VariantMask.emptyInstance(), mask1.size + mask2.size);
     }
 
     @Override

diff --git a/service/src/main/resources/application-bdc-auth.properties b/service/src/main/resources/application-bdc-auth.properties
@@ -0,0 +1,6 @@
+SMALL_JOB_LIMIT = 100
+SMALL_TASK_THREADS = 1
+LARGE_TASK_THREADS = 1
+
+hpds.genomicProcessor.impl=localPatientDistributed
+HPDS_GENOMIC_DATA_DIRECTORY=/opt/local/hpds/all/