hyracks/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/impls/LSMRTree.java

/*
 * Copyright 2009-2012 by The Regents of the University of California
 * Licensed 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 from
 * 
 *     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 edu.uci.ics.hyracks.storage.am.lsm.rtree.impls;

import java.util.List;
import java.util.ListIterator;

import edu.uci.ics.hyracks.api.dataflow.value.IBinaryComparatorFactory;
import edu.uci.ics.hyracks.api.dataflow.value.ILinearizeComparatorFactory;
import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
import edu.uci.ics.hyracks.dataflow.common.data.accessors.ITupleReference;
import edu.uci.ics.hyracks.dataflow.common.data.marshalling.IntegerSerializerDeserializer;
import edu.uci.ics.hyracks.storage.am.bloomfilter.impls.BloomCalculations;
import edu.uci.ics.hyracks.storage.am.bloomfilter.impls.BloomFilter;
import edu.uci.ics.hyracks.storage.am.bloomfilter.impls.BloomFilterFactory;
import edu.uci.ics.hyracks.storage.am.bloomfilter.impls.BloomFilterSpecification;
import edu.uci.ics.hyracks.storage.am.btree.impls.BTree;
import edu.uci.ics.hyracks.storage.am.btree.impls.BTree.BTreeAccessor;
import edu.uci.ics.hyracks.storage.am.btree.impls.RangePredicate;
import edu.uci.ics.hyracks.storage.am.common.api.IInMemoryFreePageManager;
import edu.uci.ics.hyracks.storage.am.common.api.IIndexBulkLoader;
import edu.uci.ics.hyracks.storage.am.common.api.IIndexCursor;
import edu.uci.ics.hyracks.storage.am.common.api.IModificationOperationCallback;
import edu.uci.ics.hyracks.storage.am.common.api.ISearchOperationCallback;
import edu.uci.ics.hyracks.storage.am.common.api.ISearchPredicate;
import edu.uci.ics.hyracks.storage.am.common.api.ITreeIndexAccessor;
import edu.uci.ics.hyracks.storage.am.common.api.ITreeIndexCursor;
import edu.uci.ics.hyracks.storage.am.common.api.ITreeIndexFrameFactory;
import edu.uci.ics.hyracks.storage.am.common.api.IndexException;
import edu.uci.ics.hyracks.storage.am.common.api.TreeIndexException;
import edu.uci.ics.hyracks.storage.am.common.impls.NoOpOperationCallback;
import edu.uci.ics.hyracks.storage.am.common.ophelpers.IndexOperation;
import edu.uci.ics.hyracks.storage.am.common.ophelpers.MultiComparator;
import edu.uci.ics.hyracks.storage.am.lsm.common.api.IInMemoryBufferCache;
import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMComponent;
import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMHarness;
import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIOOperation;
import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIOOperationCallback;
import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIOOperationCallbackProvider;
import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIOOperationScheduler;
import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIndexAccessorInternal;
import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIndexFileManager;
import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIndexOperationContext;
import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMMergePolicy;
import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMOperationTrackerFactory;
import edu.uci.ics.hyracks.storage.am.lsm.common.impls.LSMComponentFileReferences;
import edu.uci.ics.hyracks.storage.am.lsm.common.impls.LSMTreeIndexAccessor;
import edu.uci.ics.hyracks.storage.am.lsm.common.impls.TreeIndexFactory;
import edu.uci.ics.hyracks.storage.am.rtree.impls.RTree;
import edu.uci.ics.hyracks.storage.am.rtree.impls.RTreeSearchCursor;
import edu.uci.ics.hyracks.storage.am.rtree.impls.SearchPredicate;
import edu.uci.ics.hyracks.storage.common.buffercache.IBufferCache;
import edu.uci.ics.hyracks.storage.common.file.IFileMapProvider;

public class LSMRTree extends AbstractLSMRTree {

    public LSMRTree(IInMemoryBufferCache memBufferCache, IInMemoryFreePageManager memFreePageManager,
            ITreeIndexFrameFactory rtreeInteriorFrameFactory, ITreeIndexFrameFactory rtreeLeafFrameFactory,
            ITreeIndexFrameFactory btreeInteriorFrameFactory, ITreeIndexFrameFactory btreeLeafFrameFactory,
            ILSMIndexFileManager fileNameManager, TreeIndexFactory<RTree> diskRTreeFactory,
            TreeIndexFactory<BTree> diskBTreeFactory, BloomFilterFactory bloomFilterFactory,
            IFileMapProvider diskFileMapProvider, int fieldCount, IBinaryComparatorFactory[] rtreeCmpFactories,
            IBinaryComparatorFactory[] btreeCmpFactories, ILinearizeComparatorFactory linearizer,
            int[] comparatorFields, IBinaryComparatorFactory[] linearizerArray, ILSMMergePolicy mergePolicy,
            ILSMOperationTrackerFactory opTrackerFactory, ILSMIOOperationScheduler ioScheduler,
            ILSMIOOperationCallbackProvider ioOpCallbackProvider) {
        super(memBufferCache, memFreePageManager, rtreeInteriorFrameFactory, rtreeLeafFrameFactory,
                btreeInteriorFrameFactory, btreeLeafFrameFactory, fileNameManager, diskRTreeFactory,
                new LSMRTreeComponentFactory(diskRTreeFactory, diskBTreeFactory, bloomFilterFactory),
                diskFileMapProvider, fieldCount, rtreeCmpFactories, btreeCmpFactories, linearizer, comparatorFields,
                linearizerArray, mergePolicy, opTrackerFactory, ioScheduler, ioOpCallbackProvider);
    }

    /**
     * Opens LSMRTree, cleaning up invalid files from base dir, and registering
     * all valid files as on-disk RTrees and BTrees.
     * 
     * @param fileReference
     *            Dummy file id.
     * @throws HyracksDataException
     */
    @Override
    public synchronized void activate() throws HyracksDataException {
        super.activate();
        List<ILSMComponent> immutableComponents = componentsRef.get();
        List<LSMComponentFileReferences> validFileReferences;
        try {
            validFileReferences = fileManager.cleanupAndGetValidFiles();
        } catch (IndexException e) {
            throw new HyracksDataException(e);
        }
        immutableComponents.clear();
        for (LSMComponentFileReferences lsmComonentFileReference : validFileReferences) {
            LSMRTreeImmutableComponent component;
            try {
                component = createDiskComponent(componentFactory,
                        lsmComonentFileReference.getInsertIndexFileReference(),
                        lsmComonentFileReference.getDeleteIndexFileReference(),
                        lsmComonentFileReference.getBloomFilterFileReference(), false);
            } catch (IndexException e) {
                throw new HyracksDataException(e);
            }
            immutableComponents.add(component);
        }
        isActivated = true;
    }

    @Override
    public synchronized void deactivate(boolean flushOnExit) throws HyracksDataException {
        super.deactivate(flushOnExit);
        List<ILSMComponent> immutableComponents = componentsRef.get();
        for (ILSMComponent c : immutableComponents) {
            LSMRTreeImmutableComponent component = (LSMRTreeImmutableComponent) c;
            RTree rtree = component.getRTree();
            BTree btree = component.getBTree();
            BloomFilter bloomFilter = component.getBloomFilter();
            rtree.deactivate();
            btree.deactivate();
            bloomFilter.deactivate();
        }
        isActivated = false;
    }

    @Override
    public synchronized void deactivate() throws HyracksDataException {
        deactivate(true);
    }

    @Override
    public synchronized void destroy() throws HyracksDataException {
        super.destroy();
        List<ILSMComponent> immutableComponents = componentsRef.get();
        for (ILSMComponent c : immutableComponents) {
            LSMRTreeImmutableComponent component = (LSMRTreeImmutableComponent) c;
            component.getBTree().destroy();
            component.getBloomFilter().destroy();
            component.getRTree().destroy();
        }
        fileManager.deleteDirs();
    }

    @Override
    public synchronized void clear() throws HyracksDataException {
        super.clear();
        List<ILSMComponent> immutableComponents = componentsRef.get();
        for (ILSMComponent c : immutableComponents) {
            LSMRTreeImmutableComponent component = (LSMRTreeImmutableComponent) c;
            component.getBTree().deactivate();
            component.getBloomFilter().deactivate();
            component.getRTree().deactivate();
            component.getBTree().destroy();
            component.getBloomFilter().destroy();
            component.getRTree().destroy();
        }
        immutableComponents.clear();
    }

    @Override
    public void search(ILSMIndexOperationContext ictx, IIndexCursor cursor, ISearchPredicate pred)
            throws HyracksDataException, IndexException {
        LSMRTreeOpContext ctx = (LSMRTreeOpContext) ictx;
        List<ILSMComponent> operationalComponents = ctx.getComponentHolder();
        boolean includeMutableComponent = operationalComponents.get(0) == mutableComponent;
        int numTrees = operationalComponents.size();

        ListIterator<ILSMComponent> diskComponentIter = operationalComponents.listIterator();
        ITreeIndexAccessor[] rTreeAccessors = new ITreeIndexAccessor[numTrees];
        ITreeIndexAccessor[] bTreeAccessors = new ITreeIndexAccessor[numTrees];
        int diskComponentIx = 0;
        if (includeMutableComponent) {
            rTreeAccessors[0] = ctx.memRTreeAccessor;
            bTreeAccessors[0] = ctx.memBTreeAccessor;
            diskComponentIx++;
            diskComponentIter.next();
        }

        while (diskComponentIter.hasNext()) {
            LSMRTreeImmutableComponent component = (LSMRTreeImmutableComponent) diskComponentIter.next();
            RTree diskRTree = component.getRTree();
            BTree diskBTree = component.getBTree();
            rTreeAccessors[diskComponentIx] = diskRTree.createAccessor(NoOpOperationCallback.INSTANCE,
                    NoOpOperationCallback.INSTANCE);
            bTreeAccessors[diskComponentIx] = diskBTree.createAccessor(NoOpOperationCallback.INSTANCE,
                    NoOpOperationCallback.INSTANCE);
            diskComponentIx++;
        }

        LSMRTreeCursorInitialState initialState = new LSMRTreeCursorInitialState(numTrees, rtreeLeafFrameFactory,
                rtreeInteriorFrameFactory, btreeLeafFrameFactory, ctx.getBTreeMultiComparator(), rTreeAccessors,
                bTreeAccessors, includeMutableComponent, lsmHarness, comparatorFields, linearizerArray,
                ctx.searchCallback, operationalComponents);
        cursor.open(initialState, pred);
    }

    @Override
    public boolean scheduleFlush(ILSMIndexOperationContext ctx, ILSMIOOperationCallback callback)
            throws HyracksDataException {
        if (!mutableComponent.isModified()) {
            return false;
        }
        LSMComponentFileReferences componentFileRefs = fileManager.getRelFlushFileReference();
        ILSMIndexOperationContext rctx = createOpContext(NoOpOperationCallback.INSTANCE);
        LSMRTreeMutableComponent flushingComponent = (LSMRTreeMutableComponent) ctx.getComponentHolder().get(0);
        rctx.setOperation(IndexOperation.FLUSH);
        rctx.getComponentHolder().addAll(ctx.getComponentHolder());
        LSMRTreeAccessor accessor = new LSMRTreeAccessor(lsmHarness, rctx);
        ioScheduler.scheduleOperation(new LSMRTreeFlushOperation(accessor, flushingComponent, componentFileRefs
                .getInsertIndexFileReference(), componentFileRefs.getDeleteIndexFileReference(), componentFileRefs
                .getBloomFilterFileReference(), callback));
        return true;
    }

    @Override
    public ILSMComponent flush(ILSMIOOperation operation) throws HyracksDataException, IndexException {
        LSMRTreeFlushOperation flushOp = (LSMRTreeFlushOperation) operation;
        LSMRTreeMutableComponent flushingComponent = (LSMRTreeMutableComponent) flushOp.getFlushingComponent();
        // Renaming order is critical because we use assume ordering when we
        // read the file names when we open the tree.
        // The RTree should be renamed before the BTree.

        // scan the memory RTree
        ITreeIndexAccessor memRTreeAccessor = flushingComponent.getRTree().createAccessor(
                NoOpOperationCallback.INSTANCE, NoOpOperationCallback.INSTANCE);
        RTreeSearchCursor rtreeScanCursor = (RTreeSearchCursor) memRTreeAccessor.createSearchCursor();
        SearchPredicate rtreeNullPredicate = new SearchPredicate(null, null);
        memRTreeAccessor.search(rtreeScanCursor, rtreeNullPredicate);
        LSMRTreeImmutableComponent component = createDiskComponent(componentFactory, flushOp.getRTreeFlushTarget(),
                flushOp.getBTreeFlushTarget(), flushOp.getBloomFilterFlushTarget(), true);
        RTree diskRTree = component.getRTree();
        IIndexBulkLoader rTreeBulkloader;
        ITreeIndexCursor cursor;

        IBinaryComparatorFactory[] linearizerArray = { linearizer };

        if (rTreeTupleSorter == null) {
            rTreeTupleSorter = new TreeTupleSorter(flushingComponent.getRTree().getFileId(), linearizerArray,
                    rtreeLeafFrameFactory.createFrame(), rtreeLeafFrameFactory.createFrame(), flushingComponent
                            .getRTree().getBufferCache(), comparatorFields);
        } else {
            rTreeTupleSorter.reset();
        }
        // BulkLoad the tuples from the in-memory tree into the new disk
        // RTree.

        boolean isEmpty = true;
        try {
            while (rtreeScanCursor.hasNext()) {
                isEmpty = false;
                rtreeScanCursor.next();
                rTreeTupleSorter.insertTupleEntry(rtreeScanCursor.getPageId(), rtreeScanCursor.getTupleOffset());
            }
        } finally {
            rtreeScanCursor.close();
        }
        if (!isEmpty) {
            rTreeTupleSorter.sort();

            rTreeBulkloader = diskRTree.createBulkLoader(1.0f, false, 0L);
            cursor = rTreeTupleSorter;

            try {
                while (cursor.hasNext()) {
                    cursor.next();
                    ITupleReference frameTuple = cursor.getTuple();
                    rTreeBulkloader.add(frameTuple);
                }
            } finally {
                cursor.close();
            }
            rTreeBulkloader.end();
        }

        ITreeIndexAccessor memBTreeAccessor = flushingComponent.getBTree().createAccessor(
                NoOpOperationCallback.INSTANCE, NoOpOperationCallback.INSTANCE);
        RangePredicate btreeNullPredicate = new RangePredicate(null, null, true, true, null, null);
        IIndexCursor btreeCountingCursor = ((BTreeAccessor) memBTreeAccessor).createCountingSearchCursor();
        memBTreeAccessor.search(btreeCountingCursor, btreeNullPredicate);
        long numBTreeTuples = 0L;
        try {
            while (btreeCountingCursor.hasNext()) {
                btreeCountingCursor.next();
                ITupleReference countTuple = btreeCountingCursor.getTuple();
                numBTreeTuples = IntegerSerializerDeserializer.getInt(countTuple.getFieldData(0),
                        countTuple.getFieldStart(0));
            }
        } finally {
            btreeCountingCursor.close();
        }

        if (numBTreeTuples > 0) {
            int maxBucketsPerElement = BloomCalculations.maxBucketsPerElement(numBTreeTuples);
            BloomFilterSpecification bloomFilterSpec = BloomCalculations.computeBloomSpec(maxBucketsPerElement,
                    MAX_BLOOM_FILTER_ACCEPTABLE_FALSE_POSITIVE_RATE);

            IIndexCursor btreeScanCursor = memBTreeAccessor.createSearchCursor();
            memBTreeAccessor.search(btreeScanCursor, btreeNullPredicate);
            BTree diskBTree = component.getBTree();

            // BulkLoad the tuples from the in-memory tree into the new disk BTree.
            IIndexBulkLoader bTreeBulkloader = diskBTree.createBulkLoader(1.0f, false, numBTreeTuples);
            IIndexBulkLoader builder = component.getBloomFilter().createBuilder(numBTreeTuples,
                    bloomFilterSpec.getNumHashes(), bloomFilterSpec.getNumBucketsPerElements());
            // scan the memory BTree
            try {
                while (btreeScanCursor.hasNext()) {
                    btreeScanCursor.next();
                    ITupleReference frameTuple = btreeScanCursor.getTuple();
                    bTreeBulkloader.add(frameTuple);
                    builder.add(frameTuple);
                }
            } finally {
                btreeScanCursor.close();
                builder.end();
            }
            bTreeBulkloader.end();
        }

        return component;
    }

    @Override
    public void scheduleMerge(ILSMIndexOperationContext ctx, ILSMIOOperationCallback callback)
            throws HyracksDataException, IndexException {
        // Renaming order is critical because we use assume ordering when we
        // read the file names when we open the tree.
        // The RTree should be renamed before the BTree.
        List<ILSMComponent> mergingComponents = ctx.getComponentHolder();
        ILSMIndexOperationContext rctx = createOpContext(NoOpOperationCallback.INSTANCE);
        rctx.getComponentHolder().addAll(mergingComponents);
        ITreeIndexCursor cursor = new LSMRTreeSortedCursor(rctx, linearizer);
        ISearchPredicate rtreeSearchPred = new SearchPredicate(null, null);
        search(rctx, cursor, rtreeSearchPred);

        rctx.setOperation(IndexOperation.MERGE);
        LSMComponentFileReferences relMergeFileRefs = getMergeTargetFileName(mergingComponents);
        ILSMIndexAccessorInternal accessor = new LSMRTreeAccessor(lsmHarness, rctx);
        ioScheduler.scheduleOperation(new LSMRTreeMergeOperation((ILSMIndexAccessorInternal) accessor,
                mergingComponents, cursor, relMergeFileRefs.getInsertIndexFileReference(), relMergeFileRefs
                        .getDeleteIndexFileReference(), relMergeFileRefs.getBloomFilterFileReference(), callback));
    }

    @Override
    public ILSMComponent merge(List<ILSMComponent> mergedComponents, ILSMIOOperation operation)
            throws HyracksDataException, IndexException {
        LSMRTreeMergeOperation mergeOp = (LSMRTreeMergeOperation) operation;
        ITreeIndexCursor cursor = mergeOp.getCursor();
        mergedComponents.addAll(mergeOp.getMergingComponents());

        LSMRTreeImmutableComponent mergedComponent = createDiskComponent(componentFactory,
                mergeOp.getRTreeMergeTarget(), mergeOp.getBTreeMergeTarget(), mergeOp.getBloomFilterMergeTarget(), true);
        IIndexBulkLoader bulkLoader = mergedComponent.getRTree().createBulkLoader(1.0f, false, 0L);

        try {
            while (cursor.hasNext()) {
                cursor.next();
                ITupleReference frameTuple = cursor.getTuple();
                bulkLoader.add(frameTuple);
            }
        } finally {
            cursor.close();
        }
        bulkLoader.end();
        return mergedComponent;
    }

    @Override
    public ILSMIndexAccessorInternal createAccessor(IModificationOperationCallback modificationCallback,
            ISearchOperationCallback searchCallback) {
        return new LSMRTreeAccessor(lsmHarness, createOpContext(modificationCallback));
    }

    public class LSMRTreeAccessor extends LSMTreeIndexAccessor {
        public LSMRTreeAccessor(ILSMHarness lsmHarness, ILSMIndexOperationContext ctx) {
            super(lsmHarness, ctx);
        }

        @Override
        public ITreeIndexCursor createSearchCursor() {
            return new LSMRTreeSearchCursor(ctx);
        }

        public MultiComparator getMultiComparator() {
            LSMRTreeOpContext concreteCtx = (LSMRTreeOpContext) ctx;
            return concreteCtx.rtreeOpContext.cmp;
        }
    }

    private ILSMComponent createBulkLoadTarget() throws HyracksDataException, IndexException {
        LSMComponentFileReferences componentFileRefs = fileManager.getRelFlushFileReference();
        return createDiskComponent(componentFactory, componentFileRefs.getInsertIndexFileReference(),
                componentFileRefs.getDeleteIndexFileReference(), componentFileRefs.getBloomFilterFileReference(), true);
    }

    @Override
    public IIndexBulkLoader createBulkLoader(float fillLevel, boolean verifyInput, long numElementsHint)
            throws TreeIndexException {
        return new LSMRTreeBulkLoader(fillLevel, verifyInput, numElementsHint);
    }

    public class LSMRTreeBulkLoader implements IIndexBulkLoader {
        private final ILSMComponent component;
        private final IIndexBulkLoader bulkLoader;

        public LSMRTreeBulkLoader(float fillFactor, boolean verifyInput, long numElementsHint)
                throws TreeIndexException {
            // Note that by using a flush target file name, we state that the
            // new bulk loaded tree is "newer" than any other merged tree.
            try {
                component = createBulkLoadTarget();
            } catch (HyracksDataException e) {
                throw new TreeIndexException(e);
            } catch (IndexException e) {
                throw new TreeIndexException(e);
            }
            bulkLoader = ((LSMRTreeImmutableComponent) component).getRTree().createBulkLoader(fillFactor, verifyInput,
                    numElementsHint);
        }

        @Override
        public void add(ITupleReference tuple) throws HyracksDataException, IndexException {
            try {
                bulkLoader.add(tuple);
            } catch (IndexException e) {
                handleException();
                throw e;
            } catch (HyracksDataException e) {
                handleException();
                throw e;
            } catch (RuntimeException e) {
                handleException();
                throw e;
            }
        }

        @Override
        public void end() throws HyracksDataException, IndexException {
            bulkLoader.end();
            lsmHarness.addBulkLoadedComponent(component);
        }

        protected void handleException() throws HyracksDataException {
            ((LSMRTreeImmutableComponent) component).getRTree().deactivate();
            ((LSMRTreeImmutableComponent) component).getRTree().destroy();
            ((LSMRTreeImmutableComponent) component).getBTree().deactivate();
            ((LSMRTreeImmutableComponent) component).getBTree().destroy();
            ((LSMRTreeImmutableComponent) component).getBloomFilter().deactivate();
            ((LSMRTreeImmutableComponent) component).getBloomFilter().destroy();
        }
    }

    @Override
    public void markAsValid(ILSMComponent lsmComponent) throws HyracksDataException {
        LSMRTreeImmutableComponent component = (LSMRTreeImmutableComponent) lsmComponent;
        // Flush the bloom filter first.
        int fileId = component.getBloomFilter().getFileId();
        IBufferCache bufferCache = component.getBTree().getBufferCache();
        int startPage = 0;
        int maxPage = component.getBloomFilter().getNumPages();
        forceFlushDirtyPages(bufferCache, fileId, startPage, maxPage);
        forceFlushDirtyPages(component.getRTree());
        markAsValidInternal(component.getRTree());
        forceFlushDirtyPages(component.getBTree());
        markAsValidInternal(component.getBTree());
    }
}