storage: ALTER VIEW DROP COLUMN not supported on phoenix 5.1.x #TASK-…

…5663
opencb · Feb 20, 2024 · 9bba168 · 9bba168
1 parent 2011121
commit 9bba168
Show file tree

Hide file tree

Showing 6 changed files with 30 additions and 4 deletions.
diff --git a/...n/java/org/opencb/opencga/storage/hadoop/variant/annotation/phoenix/PhoenixCompatApi.java b/...n/java/org/opencb/opencga/storage/hadoop/variant/annotation/phoenix/PhoenixCompatApi.java
@@ -16,4 +16,6 @@ public interface PhoenixCompatApi {
 
     <T extends DBWritable> PhoenixRecordReader<T> newPhoenixRecordReader(
             Class<T> inputClass, Configuration configuration, QueryPlan queryPlan);
+
+    boolean isDropColumnFromViewSupported();
 }
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
@@ -32,4 +32,9 @@ public <T extends DBWritable> PhoenixRecordReader<T> newPhoenixRecordReader(Clas
             throw new IllegalStateException(e);
         }
     }
+
+    @Override
+    public boolean isDropColumnFromViewSupported() {
+        return true;
+    }
 }
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
@@ -23,4 +23,8 @@ public <T extends DBWritable> PhoenixRecordReader<T> newPhoenixRecordReader(Clas
         return new PhoenixRecordReader<>(inputClass, configuration, queryPlan);
     }
 
+    @Override
+    public boolean isDropColumnFromViewSupported() {
+        return true;
+    }
 }
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
@@ -41,4 +41,11 @@ public <T extends DBWritable> PhoenixRecordReader<T> newPhoenixRecordReader(Clas
         }
     }
 
+    @Override
+    public boolean isDropColumnFromViewSupported() {
+        // Phoenix 5.1.x does not support drop column from view.
+        // Might be related with https://issues.apache.org/jira/browse/PHOENIX-6025
+        return false;
+    }
+
 }
diff --git a/...c/main/java/org/opencb/opencga/storage/hadoop/variant/adaptors/phoenix/PhoenixHelper.java b/...c/main/java/org/opencb/opencga/storage/hadoop/variant/adaptors/phoenix/PhoenixHelper.java
@@ -43,6 +43,7 @@
 import org.opencb.opencga.core.common.BatchUtils;
 import org.opencb.opencga.core.common.ExceptionUtils;
 import org.opencb.opencga.core.common.TimeUtils;
+import org.opencb.opencga.storage.hadoop.HBaseCompat;
 import org.opencb.opencga.storage.hadoop.utils.HBaseManager;
 import org.opencb.opencga.storage.hadoop.variant.GenomeHelper;
 import org.slf4j.Logger;
@@ -255,6 +256,12 @@ public String buildAlterDropColumns(String tableName, Collection<CharSequence> c
     public void dropColumns(Connection con, String tableName, Collection<CharSequence> columns, PTableType tableType)
             throws SQLException {
 
+        if (!HBaseCompat.getInstance().getPhoenixCompat().isDropColumnFromViewSupported()) {
+            logger.info("Dropping columns is not supported for Phoenix version {}.{} . Skipping drop columns.",
+                    PhoenixDriver.INSTANCE.getMajorVersion(), PhoenixDriver.INSTANCE.getMinorVersion());
+            return;
+        }
+
         Set<String> existingColumns = getColumns(con, tableName, tableType)
                 .stream()
                 .map(Column::column)

diff --git a/...va/org/opencb/opencga/storage/hadoop/variant/HadoopVariantStorageEngineSplitDataTest.java b/...va/org/opencb/opencga/storage/hadoop/variant/HadoopVariantStorageEngineSplitDataTest.java
@@ -352,18 +352,19 @@ public void testDuplicatedVariantsAccepted(String... files) throws Exception {
             for (Boolean nativeQuery : Arrays.asList(true, false)) {
                 String name = fileMetadata.getName();
                 Query query = new Query(VariantQueryParam.FILE.key(), name);
+                QueryOptions options = new QueryOptions(NATIVE, nativeQuery);
                 System.out.println("-----------------------");
-                System.out.println("FILE-QUERY = " + query.toJson());
-                for (Variant variant : variantStorageEngine.get(query, new QueryOptions(NATIVE, nativeQuery)).getResults()) {
+                System.out.println("FILE-QUERY = " + query.toJson() + " " + options.toJson());
+                for (Variant variant : variantStorageEngine.get(query, new QueryOptions(options)).getResults()) {
                     StudyEntry studyEntry = variant.getStudies().get(0);
                     assertEquals(0, studyEntry.getIssues().size());
                     assertEquals(name, studyEntry.getFiles().get(0).getFileId());
                 }
                 for (Integer sample : fileMetadata.getSamples()) {
                     String sampleName = metadataManager.getSampleName(studyId, sample);
                     query = new Query(VariantQueryParam.FILE.key(), name).append(VariantQueryParam.SAMPLE.key(), sampleName);
-                    System.out.println("SAMPLE-QUERY = " + query.toJson());
-                    for (Variant variant : variantStorageEngine.get(query, new QueryOptions(NATIVE, nativeQuery)).getResults()) {
+                    System.out.println("SAMPLE-QUERY = " + query.toJson() + " " + options.toJson());
+                    for (Variant variant : variantStorageEngine.get(query, new QueryOptions(options)).getResults()) {
                         StudyEntry studyEntry = variant.getStudies().get(0);
                         assertEquals(0, studyEntry.getIssues().size());
                         assertEquals(name, studyEntry.getFiles().get(0).getFileId());