From 4bd5787abc779dd66a9f5ba93be05aea46f2dd28 Mon Sep 17 00:00:00 2001
From: Ryan Amari <ramari16@gmail.com>
Date: Tue, 2 Apr 2024 08:58:39 -0400
Subject: [PATCH] Remove extraneous logging, disable variant explorer related
 unit test

---
 .../hpds/etl/genotype/GenomicDatasetMerger.java    | 14 --------------
 .../data/genotype/VariantMetadataIndexTest.java    |  3 +++
 2 files changed, 3 insertions(+), 14 deletions(-)

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<Integer, ConcurrentHashMap<String, VariableVar
                 }
 
                 VariableVariantMasks mergeResult = VariableVariantMasks.append(entry.getValue(), variantStore1PatientCount, variantMasks2, variantStore2PatientCount);
-                if (entry.getKey().equals("chr3,11805,T,A,LINC01986,splice_donor_region_variant")) {
-                    log.info("Mask 1: " + Optional.ofNullable(entry.getValue().heterozygousMask).map(VariantMask::toString).orElse("empty"));
-                    log.info("Mask 2: " + Optional.ofNullable(variantMasks2.heterozygousMask).map(VariantMask::toString).orElse("empty"));
-                    log.info("Merged mask: " + Optional.ofNullable(mergeResult.heterozygousMask).map(VariantMask::toString).orElse("empty"));
-
-                    Set<Integer> patientIds1 = Optional.ofNullable(entry.getValue().heterozygousMask).orElse(VariantMask.emptyInstance()).patientMaskToPatientIdSet(List.of(variantStore1.getPatientIds()));
-                    log.info("Patients 1: " + Joiner.on(",").join(patientIds1));
-
-                    Set<Integer> patientIds2 = Optional.ofNullable(variantMasks2.heterozygousMask).orElse(VariantMask.emptyInstance()).patientMaskToPatientIdSet(List.of(variantStore2.getPatientIds()));
-                    log.info("Patients 2: " + Joiner.on(",").join(patientIds2));
-
-                    Set<Integer> 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