From 60b74ab3644af602be07f5b52b4a1d37393d352e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= <jacobo167@gmail.com>
Date: Wed, 20 Sep 2023 16:36:37 +0100
Subject: [PATCH] storage: Fix NPE executing SampleIndexDuplicatedVariantsTest
 tests. #TASK-5027

---
 .../SampleIndexOnlyVariantQueryExecutor.java  | 20 ++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java
index 5829a9580a8..510085420dd 100644
--- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java
+++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java
@@ -248,11 +248,7 @@ private boolean isIncludeCovered(SampleIndexQuery sampleIndexQuery, Query inputQ
                 return false;
             }
 
-            List<String> sampleDataKeys = VariantQueryUtils.getIncludeSampleData(inputQuery);
-            if (sampleDataKeys == null) {
-                // Undefined, get default sampleDataKeys
-                sampleDataKeys = HBaseToVariantConverter.getFixedFormat(study.getStudyMetadata());
-            }
+            List<String> sampleDataKeys = getSampleDataKeys(inputQuery, study);
 
             if (sampleDataKeys.size() != 1) {
                 // One and only one sampledatakey
@@ -490,8 +486,9 @@ private class AddMissingDataTask implements Task<Variant, Variant> {
             for (Integer fileId : fileIds) {
                 filesFromSample.add(metadataManager.getFileName(studyId, fileId));
             }
-            List<String> includeSampleData = VariantQueryUtils.getIncludeSampleData(parsedQuery.getInputQuery());
-            gtIdx = includeSampleData.indexOf("GT");
+
+            List<String> sampleDataKeys = getSampleDataKeys(parsedQuery.getInputQuery(), parsedQuery.getProjection().getStudy(studyId));
+            gtIdx = sampleDataKeys.indexOf("GT");
         }
 
         @Override
@@ -657,4 +654,13 @@ private void mergeFileEntries(StudyEntry studyEntry, List<FileEntry> newFileEntr
             }
         }
     }
+
+    private List<String> getSampleDataKeys(Query parsedQuery, VariantQueryProjection.StudyVariantQueryProjection parsedQuery1) {
+        List<String> sampleDataKeys = VariantQueryUtils.getIncludeSampleData(parsedQuery);
+        if (sampleDataKeys == null) {
+            // Undefined, get default sampleDataKeys
+            sampleDataKeys = HBaseToVariantConverter.getFixedFormat(parsedQuery1.getStudyMetadata());
+        }
+        return sampleDataKeys;
+    }
 }