Ensure fully deleted segments are accounted for correctly

We can't rely on the leaf reader ordinal in a wrapped reader since
it might not correspond to the ordinal in the SegmentInfos for it's
SegmentCommitInfo.

Relates to #32844
Closes #33689

x-pack/plugin/core/src/main/java/org/elasticsearch/snapshots/SourceOnlySnapshot.java

@@ -81,15 +81,25 @@ public synchronized List<String> syncSnapshot(IndexCommit commit) throws IOExcep
         try (Lock writeLock = targetDirectory.obtainLock(IndexWriter.WRITE_LOCK_NAME);
              StandardDirectoryReader reader = (StandardDirectoryReader) DirectoryReader.open(commit)) {
             SegmentInfos segmentInfos = reader.getSegmentInfos();
-            DirectoryReader wrapper = wrapReader(reader);
             List<SegmentCommitInfo> newInfos = new ArrayList<>();
-            for (LeafReaderContext ctx : wrapper.leaves()) {
-                SegmentCommitInfo info = segmentInfos.info(ctx.ord);
+            for (LeafReaderContext ctx : reader.leaves()) {
                 LeafReader leafReader = ctx.reader();
-                LiveDocs liveDocs = getLiveDocs(leafReader);
-                if (leafReader.numDocs() != 0) { // fully deleted segments don't need to be processed
-                    SegmentCommitInfo newInfo = syncSegment(info, liveDocs, leafReader.getFieldInfos(), existingSegments, createdFiles);
-                    newInfos.add(newInfo);
+                SegmentCommitInfo info = reader.getSegmentInfos().info(ctx.ord);
+                assert info.info.equals(Lucene.segmentReader(ctx.reader()).getSegmentInfo().info);
+                /* We could do this totally different without wrapping this dummy directory reader if FilterCodecReader would have a
+                 * getDelegate method. This is fixed in LUCENE-8502 but we need to wait for it to come in 7.5.1 or 7.6.
+                 * The reason here is that the ctx.ord is not guaranteed to be equivalent to the SegmentCommitInfo ord in the SegmentInfo
+                 * object since we might drop fully deleted segments. if that happens we are using the wrong reader for the SI and
+                 * might almost certainly expose deleted documents.
+                 */
+                DirectoryReader wrappedReader = wrapReader(new DummyDirectoryReader(reader.directory(), leafReader));
+                if (wrappedReader.leaves().isEmpty() == false) {
+                    leafReader = wrappedReader.leaves().get(0).reader();
+                    LiveDocs liveDocs = getLiveDocs(leafReader);
+                    if (leafReader.numDocs() != 0) { // fully deleted segments don't need to be processed
+                        SegmentCommitInfo newInfo = syncSegment(info, liveDocs, leafReader.getFieldInfos(), existingSegments, createdFiles);
+                        newInfos.add(newInfo);
+                    }
                 }
             }
             segmentInfos.clear();
@@ -257,4 +267,51 @@ private static class LiveDocs {
             this.bits = bits;
         }
     }
+
+    private static class DummyDirectoryReader extends DirectoryReader {
+
+        protected DummyDirectoryReader(Directory directory, LeafReader... segmentReaders) throws IOException {
+            super(directory, segmentReaders);
+        }
+
+        @Override
+        protected DirectoryReader doOpenIfChanged() throws IOException {
+            return null;
+        }
+
+        @Override
+        protected DirectoryReader doOpenIfChanged(IndexCommit commit) throws IOException {
+            return null;
+        }
+
+        @Override
+        protected DirectoryReader doOpenIfChanged(IndexWriter writer, boolean applyAllDeletes) throws IOException {
+            return null;
+        }
+
+        @Override
+        public long getVersion() {
+            return 0;
+        }
+
+        @Override
+        public boolean isCurrent() throws IOException {
+            return false;
+        }
+
+        @Override
+        public IndexCommit getIndexCommit() throws IOException {
+            return null;
+        }
+
+        @Override
+        protected void doClose() throws IOException {
+
+        }
+
+        @Override
+        public CacheHelper getReaderCacheHelper() {
+            return null;
+        }
+    }
 }

x-pack/plugin/core/src/main/java/org/elasticsearch/snapshots/SourceOnlySnapshotRepository.java

@@ -130,7 +130,7 @@ protected void closeInternal() {
             SourceOnlySnapshot snapshot = new SourceOnlySnapshot(tempStore.directory(), querySupplier);
             snapshot.syncSnapshot(snapshotIndexCommit);
             // we will use the lucene doc ID as the seq ID so we set the local checkpoint to maxDoc with a new index UUID
-            SegmentInfos segmentInfos = store.readLastCommittedSegmentsInfo();
+            SegmentInfos segmentInfos = tempStore.readLastCommittedSegmentsInfo();
             tempStore.bootstrapNewHistory(segmentInfos.totalMaxDoc());
             store.incRef();
             try (DirectoryReader reader = DirectoryReader.open(tempStore.directory())) {

x-pack/plugin/core/src/test/java/org/elasticsearch/snapshots/SourceOnlySnapshotIT.java

@@ -49,7 +49,7 @@
 import java.util.Map;
 import java.util.Optional;
 import java.util.concurrent.ExecutionException;
-import java.util.function.Consumer;
+import java.util.function.BiConsumer;
 
 import static org.elasticsearch.common.xcontent.XContentFactory.jsonBuilder;
 import static org.elasticsearch.test.hamcrest.ElasticsearchAssertions.assertAcked;
@@ -97,7 +97,10 @@ public void testSnapshotAndRestore() throws Exception {
         boolean requireRouting = randomBoolean();
         boolean useNested = randomBoolean();
         IndexRequestBuilder[] builders = snashotAndRestore(sourceIdx, 1, true, requireRouting, useNested);
-        assertHits(sourceIdx, builders.length);
+        IndicesStatsResponse indicesStatsResponse = client().admin().indices().prepareStats(sourceIdx).clear().setDocs(true).get();
+        long deleted = indicesStatsResponse.getTotal().docs.getDeleted();
+        boolean sourceHadDeletions = deleted > 0; // we use indexRandom which might create holes ie. deleted docs
+        assertHits(sourceIdx, builders.length, sourceHadDeletions);
         assertMappings(sourceIdx, requireRouting, useNested);
         SearchPhaseExecutionException e = expectThrows(SearchPhaseExecutionException.class, () -> {
             client().prepareSearch(sourceIdx).setQuery(QueryBuilders.idsQuery()
@@ -116,7 +119,7 @@ public void testSnapshotAndRestore() throws Exception {
             client().admin().indices().prepareUpdateSettings(sourceIdx)
                 .setSettings(Settings.builder().put("index.number_of_replicas", 1)).get();
         ensureGreen(sourceIdx);
-        assertHits(sourceIdx, builders.length);
+        assertHits(sourceIdx, builders.length, sourceHadDeletions);
     }
 
     public void testSnapshotAndRestoreWithNested() throws Exception {
@@ -125,7 +128,7 @@ public void testSnapshotAndRestoreWithNested() throws Exception {
         IndexRequestBuilder[] builders = snashotAndRestore(sourceIdx, 1, true, requireRouting, true);
         IndicesStatsResponse indicesStatsResponse = client().admin().indices().prepareStats().clear().setDocs(true).get();
         assertThat(indicesStatsResponse.getTotal().docs.getDeleted(), Matchers.greaterThan(0L));
-        assertHits(sourceIdx, builders.length);
+        assertHits(sourceIdx, builders.length, true);
         assertMappings(sourceIdx, requireRouting, true);
         SearchPhaseExecutionException e = expectThrows(SearchPhaseExecutionException.class, () ->
             client().prepareSearch(sourceIdx).setQuery(QueryBuilders.idsQuery().addIds("" + randomIntBetween(0, builders.length))).get());
@@ -141,7 +144,7 @@ public void testSnapshotAndRestoreWithNested() throws Exception {
         client().admin().indices().prepareUpdateSettings(sourceIdx).setSettings(Settings.builder().put("index.number_of_replicas", 1))
             .get();
         ensureGreen(sourceIdx);
-        assertHits(sourceIdx, builders.length);
+        assertHits(sourceIdx, builders.length, true);
     }
 
     private void assertMappings(String sourceIdx, boolean requireRouting, boolean useNested) throws IOException {
@@ -165,15 +168,12 @@ private void assertMappings(String sourceIdx, boolean requireRouting, boolean us
         }
     }
 
-    private void assertHits(String index, int numDocsExpected) {
+    private void assertHits(String index, int numDocsExpected, boolean sourceHadDeletions) {
         SearchResponse searchResponse = client().prepareSearch(index)
             .addSort(SeqNoFieldMapper.NAME, SortOrder.ASC)
             .setSize(numDocsExpected).get();
-        Consumer<SearchResponse> assertConsumer = res -> {
+        BiConsumer<SearchResponse, Boolean> assertConsumer = (res, allowHoles) -> {
             SearchHits hits = res.getHits();
-            IndicesStatsResponse indicesStatsResponse = client().admin().indices().prepareStats().clear().setDocs(true).get();
-            long deleted = indicesStatsResponse.getTotal().docs.getDeleted();
-            boolean allowHoles = deleted > 0; // we use indexRandom which might create holes ie. deleted docs
             long i = 0;
             for (SearchHit hit : hits) {
                 String id = hit.getId();
@@ -190,18 +190,24 @@ private void assertHits(String index, int numDocsExpected) {
                 assertEquals("r" + id, hit.field("_routing").getValue());
             }
         };
-        assertConsumer.accept(searchResponse);
+        assertConsumer.accept(searchResponse, sourceHadDeletions);
         assertEquals(numDocsExpected, searchResponse.getHits().totalHits);
         searchResponse = client().prepareSearch(index)
             .addSort(SeqNoFieldMapper.NAME, SortOrder.ASC)
             .setScroll("1m")
             .slice(new SliceBuilder(SeqNoFieldMapper.NAME, randomIntBetween(0,1), 2))
             .setSize(randomIntBetween(1, 10)).get();
-        do {
-            // now do a scroll with a slice
-            assertConsumer.accept(searchResponse);
-            searchResponse = client().prepareSearchScroll(searchResponse.getScrollId()).setScroll(TimeValue.timeValueMinutes(1)).get();
-        } while (searchResponse.getHits().getHits().length > 0);
+        try {
+            do {
+                // now do a scroll with a slice
+                assertConsumer.accept(searchResponse, true);
+                searchResponse = client().prepareSearchScroll(searchResponse.getScrollId()).setScroll(TimeValue.timeValueMinutes(1)).get();
+            } while (searchResponse.getHits().getHits().length > 0);
+        } finally {
+            if (searchResponse.getScrollId() != null) {
+                client().prepareClearScroll().addScrollId(searchResponse.getScrollId()).get();
+            }
+        }
 
     }
 

x-pack/plugin/core/src/test/java/org/elasticsearch/snapshots/SourceOnlySnapshotShardTests.java

@@ -162,7 +162,6 @@ private String randomDoc() {
         return "{ \"value\" : \"" + randomAlphaOfLength(10) + "\"}";
     }
 
-    @AwaitsFix(bugUrl = "https://github.com/elastic/elasticsearch/issues/33689")
     public void testRestoreMinmal() throws IOException {
         IndexShard shard = newStartedShard(true);
         int numInitialDocs = randomIntBetween(10, 100);

x-pack/plugin/core/src/test/java/org/elasticsearch/snapshots/SourceOnlySnapshotTests.java

@@ -12,10 +12,12 @@
 import org.apache.lucene.document.StoredField;
 import org.apache.lucene.document.StringField;
 import org.apache.lucene.document.TextField;
+import org.apache.lucene.index.CodecReader;
 import org.apache.lucene.index.DirectoryReader;
 import org.apache.lucene.index.FilterMergePolicy;
 import org.apache.lucene.index.IndexCommit;
 import org.apache.lucene.index.IndexFileNames;
+import org.apache.lucene.index.IndexReader;
 import org.apache.lucene.index.IndexWriter;
 import org.apache.lucene.index.IndexWriterConfig;
 import org.apache.lucene.index.KeepOnlyLastCommitDeletionPolicy;
@@ -34,6 +36,7 @@
 import org.apache.lucene.search.TermQuery;
 import org.apache.lucene.search.TopDocs;
 import org.apache.lucene.store.Directory;
+import org.apache.lucene.util.IOSupplier;
 import org.elasticsearch.common.lucene.Lucene;
 import org.elasticsearch.test.ESTestCase;
 
@@ -242,4 +245,55 @@ public boolean useCompoundFile(SegmentInfos infos, SegmentCommitInfo mergedInfo,
             reader.close();
         }
     }
+
+    public void testFullyDeletedSegments() throws IOException {
+        try (Directory dir = newDirectory()) {
+            SnapshotDeletionPolicy deletionPolicy = new SnapshotDeletionPolicy(new KeepOnlyLastCommitDeletionPolicy());
+            IndexWriter writer = new IndexWriter(dir, newIndexWriterConfig()
+                .setSoftDeletesField(Lucene.SOFT_DELETES_FIELD)
+                .setIndexDeletionPolicy(deletionPolicy).setMergePolicy(new FilterMergePolicy(NoMergePolicy.INSTANCE) {
+                    @Override
+                    public boolean useCompoundFile(SegmentInfos infos, SegmentCommitInfo mergedInfo, MergeContext mergeContext) {
+                        return randomBoolean();
+                    }
+
+                    @Override
+                    public boolean keepFullyDeletedSegment(IOSupplier<CodecReader> readerIOSupplier) throws IOException {
+                        return true;
+                    }
+                }));
+            Document doc = new Document();
+            doc.add(new StringField("id", "1", Field.Store.YES));
+            doc.add(new TextField("text", "the quick brown fox", Field.Store.NO));
+            doc.add(new NumericDocValuesField("rank", 1));
+            doc.add(new StoredField("rank", 1));
+            doc.add(new StoredField("src", "the quick brown fox"));
+            writer.addDocument(doc);
+            writer.commit();
+            doc = new Document();
+            doc.add(new StringField("id", "1", Field.Store.YES));
+            doc.add(new TextField("text", "the quick brown fox", Field.Store.NO));
+            doc.add(new NumericDocValuesField("rank", 3));
+            doc.add(new StoredField("rank", 3));
+            doc.add(new StoredField("src", "the quick brown fox"));
+            writer.softUpdateDocument(new Term("id", "1"), doc, new NumericDocValuesField(Lucene.SOFT_DELETES_FIELD, 1));
+            writer.commit();
+            try (Directory targetDir = newDirectory()) {
+                IndexCommit snapshot = deletionPolicy.snapshot();
+                SourceOnlySnapshot snapshoter = new SourceOnlySnapshot(targetDir);
+                snapshoter.syncSnapshot(snapshot);
+
+                try (DirectoryReader snapReader = DirectoryReader.open(targetDir)) {
+                    assertEquals(snapReader.maxDoc(), 1);
+                    assertEquals(snapReader.numDocs(), 1);
+                    assertEquals("3", snapReader.document(0).getField("rank").stringValue());
+                }
+                try (IndexReader writerReader = DirectoryReader.open(writer)) {
+                    assertEquals(writerReader.maxDoc(), 2);
+                    assertEquals(writerReader.numDocs(), 1);
+                }
+            }
+            writer.close();
+        }
+    }
 }