diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java index 760516cb..ae3a06e6 100644 --- a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java +++ b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java @@ -246,20 +246,6 @@ public FileBackedJsonIndexStorage patientIds1 = Optional.ofNullable(entry.getValue().heterozygousMask).orElse(VariantMask.emptyInstance()).patientMaskToPatientIdSet(List.of(variantStore1.getPatientIds())); - log.info("Patients 1: " + Joiner.on(",").join(patientIds1)); - - Set patientIds2 = Optional.ofNullable(variantMasks2.heterozygousMask).orElse(VariantMask.emptyInstance()).patientMaskToPatientIdSet(List.of(variantStore2.getPatientIds())); - log.info("Patients 2: " + Joiner.on(",").join(patientIds2)); - - Set mergedPatientIds = Optional.ofNullable(mergeResult.heterozygousMask).orElse(VariantMask.emptyInstance()).patientMaskToPatientIdSet(List.of(mergedVariantStore.getPatientIds())); - log.info("Merged patient ids: " + Joiner.on(",").join(mergedPatientIds)); - } mergedMasks.put(entry.getKey(), mergeResult); } // Any entry in the second set that is not in the merged set can be merged with an empty variant mask, diff --git a/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMetadataIndexTest.java b/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMetadataIndexTest.java index df340f84..58e1d48a 100644 --- a/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMetadataIndexTest.java +++ b/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMetadataIndexTest.java @@ -9,6 +9,7 @@ import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; import edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.VariantMetadataLoader; import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; import org.springframework.test.context.event.annotation.BeforeTestClass; @@ -16,6 +17,8 @@ import static org.springframework.test.util.AssertionErrors.assertEquals; import static org.springframework.test.util.AssertionErrors.assertNotNull; +// todo: enable when variant explorer is implemented +@Disabled public class VariantMetadataIndexTest { //From file 1 14 19038291 rs550062154 C A