Merge branch 'master' into reject-empty-id

* master:
  Use sequence numbers to identify out of order delivery in replicas & recovery (elastic#24060)
  Remove customization of ES_USER and ES_GROUP

core/src/main/java/org/elasticsearch/common/lucene/uid/PerThreadIDAndVersionLookup.java → core/src/main/java/org/elasticsearch/common/lucene/uid/PerThreadIDVersionAndSeqNoLookup.java

@@ -29,9 +29,12 @@
 import org.apache.lucene.search.DocIdSetIterator;
 import org.apache.lucene.util.Bits;
 import org.apache.lucene.util.BytesRef;
-import org.elasticsearch.common.lucene.uid.VersionsResolver.DocIdAndVersion;
+import org.elasticsearch.common.lucene.uid.VersionsAndSeqNoResolver.DocIdAndSeqNo;
+import org.elasticsearch.common.lucene.uid.VersionsAndSeqNoResolver.DocIdAndVersion;
+import org.elasticsearch.index.mapper.SeqNoFieldMapper;
 import org.elasticsearch.index.mapper.UidFieldMapper;
 import org.elasticsearch.index.mapper.VersionFieldMapper;
+import org.elasticsearch.index.seqno.SequenceNumbersService;
 
 import java.io.IOException;
 
@@ -43,15 +46,18 @@
  *  in more than one document!  It will only return the first one it
  *  finds. */
 
-final class PerThreadIDAndVersionLookup {
+final class PerThreadIDVersionAndSeqNoLookup {
     // TODO: do we really need to store all this stuff? some if it might not speed up anything.
     // we keep it around for now, to reduce the amount of e.g. hash lookups by field and stuff
 
     /** terms enum for uid field */
     private final TermsEnum termsEnum;
     /** _version data */
     private final NumericDocValues versions;
-
+    /** _seq_no data */
+    private final NumericDocValues seqNos;
+    /** _primary_term data */
+    private final NumericDocValues primaryTerms;
     /** Reused for iteration (when the term exists) */
     private PostingsEnum docsEnum;
 
@@ -61,7 +67,7 @@ final class PerThreadIDAndVersionLookup {
     /**
      * Initialize lookup for the provided segment
      */
-    PerThreadIDAndVersionLookup(LeafReader reader) throws IOException {
+    PerThreadIDVersionAndSeqNoLookup(LeafReader reader) throws IOException {
         Fields fields = reader.fields();
         Terms terms = fields.terms(UidFieldMapper.NAME);
         termsEnum = terms.iterator();
@@ -74,6 +80,8 @@ final class PerThreadIDAndVersionLookup {
             throw new IllegalArgumentException("reader misses the [" + VersionFieldMapper.NAME +
                 "] field");
         }
+        seqNos = reader.getNumericDocValues(SeqNoFieldMapper.NAME);
+        primaryTerms = reader.getNumericDocValues(SeqNoFieldMapper.PRIMARY_TERM_NAME);
         Object readerKey = null;
         assert (readerKey = reader.getCoreCacheKey()) != null;
         this.readerKey = readerKey;
@@ -113,4 +121,25 @@ private int getDocID(BytesRef id, Bits liveDocs) throws IOException {
             return DocIdSetIterator.NO_MORE_DOCS;
         }
     }
+
+    /** Return null if id is not found. */
+    DocIdAndSeqNo lookupSeqNo(BytesRef id, Bits liveDocs, LeafReaderContext context) throws IOException {
+        assert context.reader().getCoreCacheKey().equals(readerKey) :
+            "context's reader is not the same as the reader class was initialized on.";
+        int docID = getDocID(id, liveDocs);
+        if (docID != DocIdSetIterator.NO_MORE_DOCS) {
+            return new DocIdAndSeqNo(docID, seqNos == null ? SequenceNumbersService.UNASSIGNED_SEQ_NO : seqNos.get(docID), context);
+        } else {
+            return null;
+        }
+    }
+
+    /**
+     * returns 0 if the primary term is not found.
+     *
+     * Note that 0 is an illegal primary term. See {@link org.elasticsearch.cluster.metadata.IndexMetaData#primaryTerm(int)}
+     **/
+    long lookUpPrimaryTerm(int docID) throws IOException {
+            return primaryTerms == null ? 0  : primaryTerms.get(docID);
+    }
 }

core/src/main/java/org/elasticsearch/common/lucene/uid/VersionsAndSeqNoResolver.java

@@ -0,0 +1,180 @@
+/*
+ * Licensed to Elasticsearch under one or more contributor
+ * license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright
+ * ownership. Elasticsearch licenses this file to you under
+ * the Apache License, Version 2.0 (the "License"); you may
+ * not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+package org.elasticsearch.common.lucene.uid;
+
+import org.apache.lucene.index.IndexReader;
+import org.apache.lucene.index.LeafReader;
+import org.apache.lucene.index.LeafReader.CoreClosedListener;
+import org.apache.lucene.index.LeafReaderContext;
+import org.apache.lucene.index.Term;
+import org.apache.lucene.util.CloseableThreadLocal;
+import org.elasticsearch.common.util.concurrent.ConcurrentCollections;
+import org.elasticsearch.index.mapper.UidFieldMapper;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.concurrent.ConcurrentMap;
+
+import static org.elasticsearch.common.lucene.uid.Versions.NOT_FOUND;
+
+/** Utility class to resolve the Lucene doc ID, version, seqNo and primaryTerms for a given uid. */
+public final class VersionsAndSeqNoResolver {
+
+    static final ConcurrentMap<Object, CloseableThreadLocal<PerThreadIDVersionAndSeqNoLookup>> lookupStates =
+        ConcurrentCollections.newConcurrentMapWithAggressiveConcurrency();
+
+    // Evict this reader from lookupStates once it's closed:
+    private static final CoreClosedListener removeLookupState = key -> {
+        CloseableThreadLocal<PerThreadIDVersionAndSeqNoLookup> ctl = lookupStates.remove(key);
+        if (ctl != null) {
+            ctl.close();
+        }
+    };
+
+    private static PerThreadIDVersionAndSeqNoLookup getLookupState(LeafReader reader) throws IOException {
+        Object key = reader.getCoreCacheKey();
+        CloseableThreadLocal<PerThreadIDVersionAndSeqNoLookup> ctl = lookupStates.get(key);
+        if (ctl == null) {
+            // First time we are seeing this reader's core; make a new CTL:
+            ctl = new CloseableThreadLocal<>();
+            CloseableThreadLocal<PerThreadIDVersionAndSeqNoLookup> other = lookupStates.putIfAbsent(key, ctl);
+            if (other == null) {
+                // Our CTL won, we must remove it when the core is closed:
+                reader.addCoreClosedListener(removeLookupState);
+            } else {
+                // Another thread beat us to it: just use their CTL:
+                ctl = other;
+            }
+        }
+
+        PerThreadIDVersionAndSeqNoLookup lookupState = ctl.get();
+        if (lookupState == null) {
+            lookupState = new PerThreadIDVersionAndSeqNoLookup(reader);
+            ctl.set(lookupState);
+        }
+
+        return lookupState;
+    }
+
+    private VersionsAndSeqNoResolver() {
+    }
+
+    /** Wraps an {@link LeafReaderContext}, a doc ID <b>relative to the context doc base</b> and a version. */
+    public static class DocIdAndVersion {
+        public final int docId;
+        public final long version;
+        public final LeafReaderContext context;
+
+        DocIdAndVersion(int docId, long version, LeafReaderContext context) {
+            this.docId = docId;
+            this.version = version;
+            this.context = context;
+        }
+    }
+
+    /** Wraps an {@link LeafReaderContext}, a doc ID <b>relative to the context doc base</b> and a seqNo. */
+    public static class DocIdAndSeqNo {
+        public final int docId;
+        public final long seqNo;
+        public final LeafReaderContext context;
+
+        DocIdAndSeqNo(int docId, long seqNo, LeafReaderContext context) {
+            this.docId = docId;
+            this.seqNo = seqNo;
+            this.context = context;
+        }
+    }
+
+
+    /**
+     * Load the internal doc ID and version for the uid from the reader, returning<ul>
+     * <li>null if the uid wasn't found,
+     * <li>a doc ID and a version otherwise
+     * </ul>
+     */
+    public static DocIdAndVersion loadDocIdAndVersion(IndexReader reader, Term term) throws IOException {
+        assert term.field().equals(UidFieldMapper.NAME) : "unexpected term field " + term.field();
+        List<LeafReaderContext> leaves = reader.leaves();
+        if (leaves.isEmpty()) {
+            return null;
+        }
+        // iterate backwards to optimize for the frequently updated documents
+        // which are likely to be in the last segments
+        for (int i = leaves.size() - 1; i >= 0; i--) {
+            LeafReaderContext context = leaves.get(i);
+            LeafReader leaf = context.reader();
+            PerThreadIDVersionAndSeqNoLookup lookup = getLookupState(leaf);
+            DocIdAndVersion result = lookup.lookupVersion(term.bytes(), leaf.getLiveDocs(), context);
+            if (result != null) {
+                return result;
+            }
+        }
+        return null;
+    }
+
+    /**
+     * Load the internal doc ID and sequence number for the uid from the reader, returning<ul>
+     * <li>null if the uid wasn't found,
+     * <li>a doc ID and the associated seqNo otherwise
+     * </ul>
+     */
+    public static DocIdAndSeqNo loadDocIdAndSeqNo(IndexReader reader, Term term) throws IOException {
+        assert term.field().equals(UidFieldMapper.NAME) : "unexpected term field " + term.field();
+        List<LeafReaderContext> leaves = reader.leaves();
+        if (leaves.isEmpty()) {
+            return null;
+        }
+        // iterate backwards to optimize for the frequently updated documents
+        // which are likely to be in the last segments
+        for (int i = leaves.size() - 1; i >= 0; i--) {
+            LeafReaderContext context = leaves.get(i);
+            LeafReader leaf = context.reader();
+            PerThreadIDVersionAndSeqNoLookup lookup = getLookupState(leaf);
+            DocIdAndSeqNo result = lookup.lookupSeqNo(term.bytes(), leaf.getLiveDocs(), context);
+            if (result != null) {
+                return result;
+            }
+        }
+        return null;
+    }
+
+    /**
+     * Load the primaryTerm associated with the given {@link DocIdAndSeqNo}
+     */
+    public static long loadPrimaryTerm(DocIdAndSeqNo docIdAndSeqNo) throws IOException {
+        LeafReader leaf = docIdAndSeqNo.context.reader();
+        PerThreadIDVersionAndSeqNoLookup lookup = getLookupState(leaf);
+        long result = lookup.lookUpPrimaryTerm(docIdAndSeqNo.docId);
+        assert result > 0 : "should always resolve a primary term for a resolved sequence number. primary_term [" + result + "]"
+            + " docId [" + docIdAndSeqNo.docId + "] seqNo [" + docIdAndSeqNo.seqNo + "]";
+        return result;
+    }
+
+    /**
+     * Load the version for the uid from the reader, returning<ul>
+     * <li>{@link Versions#NOT_FOUND} if no matching doc exists,
+     * <li>the version associated with the provided uid otherwise
+     * </ul>
+     */
+    public static long loadVersion(IndexReader reader, Term term) throws IOException {
+        final DocIdAndVersion docIdAndVersion = loadDocIdAndVersion(reader, term);
+        return docIdAndVersion == null ? NOT_FOUND : docIdAndVersion.version;
+    }
+}