storage: Fix newPhoenixRecordReader creation at hbase-compat2.0 #TASK…

…-5663
opencb · Feb 22, 2024 · 565693f · 565693f
1 parent e8a2b4a
commit 565693f
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Showing 4 changed files with 10 additions and 23 deletions.
diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml
@@ -103,5 +103,6 @@ jobs:
           report_paths: './**/surefire-reports/TEST-*.xml'
           commit: '${{ github.sha }}'
           fail_on_test_failures: true
+          fail_if_no_tests: false
 
 
diff --git a/opencga-analysis/src/test/java/org/opencb/opencga/analysis/family/FamilyAnalysisTest.java b/opencga-analysis/src/test/java/org/opencb/opencga/analysis/family/FamilyAnalysisTest.java
@@ -96,18 +96,9 @@ public static void setUpCatalogManager(CatalogManager catalogManager) throws Cat
         studyId = catalogManager.getStudyManager().create(projectId, "phase1", null, "Phase 1", "Done", null, null, null, null, null,
                 sessionIdUser).first().getId();
 
-        try {
-            family = createDummyFamily("Martinez-Martinez").first();
-        } catch (CatalogException e) {
-        }
-        try {
-            family2 = createDummyFamily("Lopez-Lopez", Arrays.asList("father11-sample", "mother11-sample"), 1).first();
-        } catch (CatalogException e) {
-        }
-        try {
-            family3 = createDummyFamily("Perez-Perez", Arrays.asList("father22-sample", "mother22-sample", "child222-sample"), 0).first();
-        } catch (CatalogException e) {
-        }
+        family = createDummyFamily("Martinez-Martinez").first();
+        family2 = createDummyFamily("Lopez-Lopez", Arrays.asList("father11-sample", "mother11-sample"), 1).first();
+        family3 = createDummyFamily("Perez-Perez", Arrays.asList("father22-sample", "mother22-sample", "child222-sample"), 0).first();
     }
 
     @After

diff --git a/opencga-app/app/misc/solr/prepare_configsets.sh b/opencga-app/app/misc/solr/prepare_configsets.sh
@@ -1,5 +1,9 @@
 #!/bin/bash
 
+set -e
+set -o pipefail
+set -o nounset
+
 if [ $# -eq 2 ]; then
   echo $0 $@
 else
@@ -19,7 +23,7 @@ sed -i "s/REPLACEME_OPENCGA_VERSION/${VERSION}/g" "${SOLR_DIR}/INSTALL.md"
 sed -i "s/REPLACEME_OPENCGA_VERSION/${VERSION}/g" "${SOLR_DIR}/install.sh"
 
 # Iterate over the different config sets
-for name in variant rga rga-aux file sample individual family cohort job; do
+for name in variant rga rga-aux; do
   CONFIG_SET_NAME="opencga-$name-configset-$VERSION"
   CONFIG_SET_DIR="$SOLR_DIR/$CONFIG_SET_NAME"
 

diff --git a/...main/java/org/opencb/opencga/storage/hadoop/variant/annotation/phoenix/PhoenixCompat.java b/...main/java/org/opencb/opencga/storage/hadoop/variant/annotation/phoenix/PhoenixCompat.java
@@ -3,13 +3,11 @@
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.mapreduce.lib.db.DBWritable;
 import org.apache.phoenix.compile.QueryPlan;
-import org.apache.phoenix.iterate.MapReduceParallelScanGrouper;
 import org.apache.phoenix.mapreduce.PhoenixRecordReader;
 import org.apache.phoenix.schema.PColumn;
 import org.apache.phoenix.schema.PTable;
 import org.apache.phoenix.schema.PTableImpl;
 
-import java.lang.reflect.Constructor;
 import java.sql.SQLException;
 import java.util.List;
 
@@ -23,14 +21,7 @@ public PTable makePTable(List<PColumn> columns) throws SQLException {
     @Override
     public <T extends DBWritable> PhoenixRecordReader<T> newPhoenixRecordReader(Class<T> inputClass, Configuration configuration,
                                                                                 QueryPlan queryPlan) {
-        try {
-            Constructor<PhoenixRecordReader> constructor = PhoenixRecordReader.class
-                    .getConstructor(Class.class, Configuration.class, QueryPlan.class, MapReduceParallelScanGrouper.class);
-            constructor.setAccessible(true);
-            return constructor.newInstance(inputClass, configuration, queryPlan, MapReduceParallelScanGrouper.getInstance());
-        } catch (ReflectiveOperationException e) {
-            throw new IllegalStateException(e);
-        }
+        return new PhoenixRecordReader<>(inputClass, configuration, queryPlan);
     }
 
     @Override