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storage: Define start-stop row scan for deleting files from archive t…
…able. #TASK-6756
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42 changes: 42 additions & 0 deletions
42
.../java/org/opencb/opencga/storage/hadoop/variant/archive/ArchiveDeleteHBaseColumnTask.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| package org.opencb.opencga.storage.hadoop.variant.archive; | ||
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| import org.apache.hadoop.conf.Configuration; | ||
| import org.apache.hadoop.hbase.util.Bytes; | ||
| import org.apache.hadoop.hbase.util.Pair; | ||
| import org.opencb.commons.datastore.core.ObjectMap; | ||
| import org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver; | ||
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| import java.util.ArrayList; | ||
| import java.util.HashSet; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
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| public class ArchiveDeleteHBaseColumnTask extends DeleteHBaseColumnDriver.DeleteHBaseColumnTask { | ||
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| public static final String FILE_BATCHES_WITH_FILES_TO_DELETE_FROM_ARCHIVE_INDEX = "fileBatchesWithFilesToDeleteFromArchiveIndex"; | ||
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| public static void configureTask(ObjectMap options, List<Integer> fileIds) { | ||
| ArchiveRowKeyFactory keyFactory = new ArchiveRowKeyFactory(options); | ||
| Set<Integer> fileBatchesSet = new HashSet<>(); | ||
| for (Integer fileId : fileIds) { | ||
| fileBatchesSet.add(keyFactory.getFileBatch(fileId)); | ||
| } | ||
| List<Integer> fileBatches = new ArrayList<>(fileBatchesSet); | ||
| fileBatches.sort(Integer::compareTo); | ||
| options.put(DeleteHBaseColumnDriver.DELETE_HBASE_COLUMN_TASK_CLASS, ArchiveDeleteHBaseColumnTask.class.getName()); | ||
| options.put(ArchiveDeleteHBaseColumnTask.FILE_BATCHES_WITH_FILES_TO_DELETE_FROM_ARCHIVE_INDEX, fileBatches); | ||
| } | ||
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| @Override | ||
| public List<Pair<byte[], byte[]>> getRegionsToDelete(Configuration configuration) { | ||
| int[] fileBatches = configuration.getInts(FILE_BATCHES_WITH_FILES_TO_DELETE_FROM_ARCHIVE_INDEX); | ||
| List<Pair<byte[], byte[]>> regions = new ArrayList<>(); | ||
| ArchiveRowKeyFactory archiveRowKeyFactory = new ArchiveRowKeyFactory(configuration); | ||
| for (int fileBatch : fileBatches) { | ||
| regions.add(new Pair<>( | ||
| Bytes.toBytes(archiveRowKeyFactory.generateBlockIdFromBatch(fileBatch)), | ||
| Bytes.toBytes(archiveRowKeyFactory.generateBlockIdFromBatch(fileBatch + 1)))); | ||
| } | ||
| return regions; | ||
| } | ||
| } |
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59 changes: 59 additions & 0 deletions
59
...a/org/opencb/opencga/storage/hadoop/variant/archive/ArchiveDeleteHBaseColumnTaskTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| package org.opencb.opencga.storage.hadoop.variant.archive; | ||
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| import org.apache.hadoop.conf.Configuration; | ||
| import org.apache.hadoop.hbase.util.Bytes; | ||
| import org.apache.hadoop.hbase.util.Pair; | ||
| import org.junit.Assert; | ||
| import org.junit.Test; | ||
| import org.opencb.commons.datastore.core.ObjectMap; | ||
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| import java.util.Arrays; | ||
| import java.util.List; | ||
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| import static org.junit.Assert.assertArrayEquals; | ||
| import static org.junit.Assert.assertEquals; | ||
| import static org.opencb.opencga.storage.hadoop.variant.archive.ArchiveDeleteHBaseColumnTask.*; | ||
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| public class ArchiveDeleteHBaseColumnTaskTest { | ||
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| private ArchiveDeleteHBaseColumnTask task; | ||
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| @Test | ||
| public void testConfigureTask() { | ||
| ObjectMap options = new ObjectMap(); | ||
| task = new ArchiveDeleteHBaseColumnTask(); | ||
| configureTask(options, Arrays.asList(1, 2, 3)); | ||
| assertEquals(Arrays.asList(0), options.getAsIntegerList(FILE_BATCHES_WITH_FILES_TO_DELETE_FROM_ARCHIVE_INDEX)); | ||
| List<Pair<byte[], byte[]>> regionsToDelete = task.getRegionsToDelete(toConf(options)); | ||
| assertEquals(1, regionsToDelete.size()); | ||
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| assertArrayEquals(Bytes.toBytes("00000_"), regionsToDelete.get(0).getFirst()); | ||
| assertArrayEquals(Bytes.toBytes("00001_"), regionsToDelete.get(0).getSecond()); | ||
| } | ||
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| @Test | ||
| public void testConfigureTaskMultiRegions() { | ||
| ObjectMap options = new ObjectMap(); | ||
| task = new ArchiveDeleteHBaseColumnTask(); | ||
| configureTask(options, Arrays.asList(5300, 6053, 9032)); | ||
| assertEquals(Arrays.asList(5, 6, 9), options.getAsIntegerList(FILE_BATCHES_WITH_FILES_TO_DELETE_FROM_ARCHIVE_INDEX)); | ||
| List<Pair<byte[], byte[]>> regionsToDelete = task.getRegionsToDelete(toConf(options)); | ||
| assertEquals(3, regionsToDelete.size()); | ||
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| assertArrayEquals(Bytes.toBytes("00005_"), regionsToDelete.get(0).getFirst()); | ||
| assertArrayEquals(Bytes.toBytes("00006_"), regionsToDelete.get(0).getSecond()); | ||
| assertArrayEquals(Bytes.toBytes("00006_"), regionsToDelete.get(1).getFirst()); | ||
| assertArrayEquals(Bytes.toBytes("00007_"), regionsToDelete.get(1).getSecond()); | ||
| assertArrayEquals(Bytes.toBytes("00009_"), regionsToDelete.get(2).getFirst()); | ||
| assertArrayEquals(Bytes.toBytes("00010_"), regionsToDelete.get(2).getSecond()); | ||
| } | ||
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| private static Configuration toConf(ObjectMap options) { | ||
| Configuration conf = new Configuration(); | ||
| for (String key : options.keySet()) { | ||
| conf.set(key, options.getString(key)); | ||
| } | ||
| return conf; | ||
| } | ||
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| } |