From 98ff36054ae6745fea94326b956c69a42344ce45 Mon Sep 17 00:00:00 2001 From: ramari16 Date: Wed, 8 May 2024 09:17:28 -0400 Subject: [PATCH] ALS-6411: Null pointer when joining empty patient masks in GenomicProcessorPatientMergingParentImpl (#107) * ALS-6408: Cleanup bdc genomic config --- .../GenomicProcessorPatientMergingParentImpl.java | 3 ++- service/src/main/resources/application-bdc-auth.properties | 6 ++++++ 2 files changed, 8 insertions(+), 1 deletion(-) create mode 100644 service/src/main/resources/application-bdc-auth.properties diff --git a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImpl.java b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImpl.java index 253ee874..4d3b8a25 100644 --- a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImpl.java +++ b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImpl.java @@ -79,7 +79,8 @@ public Mono 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 new file mode 100644 index 00000000..860f5d64 --- /dev/null +++ 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/ \ No newline at end of file