[28/69] [abbrv] [partial] incubator-rya git commit: RYA-198 Renaming Files

[mi...@apache.org]

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/accumulo/pcj/iterators/PCJKeyToCrossProductBindingSetIterator.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/accumulo/pcj/iterators/PCJKeyToCrossProductBindingSetIterator.java b/extras/indexing/src/main/java/mvm/rya/accumulo/pcj/iterators/PCJKeyToCrossProductBindingSetIterator.java
deleted file mode 100644
index 0c7369c..0000000
--- a/extras/indexing/src/main/java/mvm/rya/accumulo/pcj/iterators/PCJKeyToCrossProductBindingSetIterator.java
+++ /dev/null
@@ -1,267 +0,0 @@
-package mvm.rya.accumulo.pcj.iterators;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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.
- */
-
-import info.aduna.iteration.CloseableIteration;
-
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.NoSuchElementException;
-import java.util.Set;
-
-import mvm.rya.indexing.external.tupleSet.ExternalTupleSet;
-
-import org.apache.accumulo.core.client.Scanner;
-import org.apache.accumulo.core.data.Key;
-import org.apache.rya.indexing.pcj.storage.accumulo.AccumuloPcjSerializer;
-import org.apache.rya.indexing.pcj.storage.accumulo.BindingSetConverter.BindingSetConversionException;
-import org.apache.rya.indexing.pcj.storage.accumulo.VariableOrder;
-import org.openrdf.model.Value;
-import org.openrdf.query.BindingSet;
-import org.openrdf.query.QueryEvaluationException;
-import org.openrdf.query.algebra.evaluation.QueryBindingSet;
-
-import com.google.common.collect.HashBiMap;
-
-/**
- *	This class takes in a {@link Scanner} and a Collection of BindingSets,
- *	deserializes each {@link Map.Entry<Key,Value>} taken from the Scanner into
- *  a {@link BindingSet}, and performs a cross product on the BindingSet with
- *  each BindingSet in the provided Collection.  The user can also specify a
- *  {@link Map<String, Value>} of constant constraints that can be used to filter.
- *
- */
-public class PCJKeyToCrossProductBindingSetIterator implements
-		CloseableIteration<BindingSet, QueryEvaluationException> {
-
-	//BindingSets passed to PCJ used to form cross product
-	private List<BindingSet> crossProductBs;
-	//Scanner over PCJ table
-	private Scanner scanner;
-	//Iterator over PCJ scanner
-	private Iterator<Map.Entry<Key, org.apache.accumulo.core.data.Value>> iterator;
-	//Map of PCJ variables in table to variable in query
-	private Map<String, String> pcjVarMap;
-	//if PCJ contains LeftJoin, this is a set of variables that only appear in
-	//LeftJoin.  Used when performing the cross product.
-	private Set<String> unAssuredVariables;
-	private final AccumuloPcjSerializer converter = new AccumuloPcjSerializer();
-	private final BindingSet EMPTY_BINDINGSET = new QueryBindingSet();
-	private Iterator<BindingSet> crossProductIter = Collections.emptyIterator();
-	private Map<String, Value> constantConstraints;
-	private BindingSet next;
-	private boolean hasNextCalled = false;
-	private boolean isEmpty = false;
-	private boolean crossProductBsExist = false;
-	private boolean constantConstraintsExist = false;
-
-	public PCJKeyToCrossProductBindingSetIterator(Scanner scanner,
-			List<BindingSet> crossProductBs,
-			Map<String, Value> constantConstraints, Set<String> unAssuredVariables,
-			Map<String, String> pcjVarMap) {
-		this.crossProductBs = crossProductBs;
-		this.scanner = scanner;
-		this.iterator = scanner.iterator();
-		this.pcjVarMap = HashBiMap.create(pcjVarMap).inverse();
-		this.constantConstraints = constantConstraints;
-		this.crossProductBsExist = crossProductBs.size() > 0;
-		this.constantConstraintsExist = constantConstraints.size() > 0;
-		this.unAssuredVariables = unAssuredVariables;
-	}
-
-	@Override
-	public boolean hasNext() throws QueryEvaluationException {
-		if (!hasNextCalled && !isEmpty) {
-			if (crossProductBsExist) {
-				while (crossProductIter.hasNext() || iterator.hasNext()) {
-					if (!crossProductIter.hasNext()) {
-						Key key = iterator.next().getKey();
-						try {
-							crossProductIter = getCrossProducts(getBindingSet(key));
-						} catch (BindingSetConversionException e) {
-							throw new QueryEvaluationException(e);
-						}
-					}
-					if (!crossProductIter.hasNext()) {
-						continue;
-					}
-					next = crossProductIter.next();
-					hasNextCalled = true;
-					return true;
-				}
-			} else {
-				while (iterator.hasNext()) {
-					Key key = iterator.next().getKey();
-					try {
-						next = getBindingSet(key);
-					} catch (BindingSetConversionException e) {
-						throw new QueryEvaluationException(e);
-					}
-					//BindingSet cannot be deserialized or is filtered
-					//out by constant constraints
-					if (next == null || next == EMPTY_BINDINGSET) {
-						continue;
-					}
-					hasNextCalled = true;
-					return true;
-				}
-			}
-			isEmpty = true;
-			return false;
-		} else if (isEmpty) {
-			return false;
-		} else {
-			return true;
-		}
-	}
-
-	@Override
-	public BindingSet next() throws QueryEvaluationException {
-		if (hasNextCalled) {
-			hasNextCalled = false;
-		} else if (isEmpty) {
-			throw new NoSuchElementException();
-		} else {
-			if (this.hasNext()) {
-				hasNextCalled = false;
-			} else {
-				throw new NoSuchElementException();
-			}
-		}
-		return next;
-	}
-
-	@Override
-	public void remove() throws QueryEvaluationException {
-		throw new UnsupportedOperationException();
-	}
-
-	@Override
-	public void close() throws QueryEvaluationException {
-		scanner.close();
-	}
-
-	/**
-	 *
-	 * @param key
-	 *            - Accumulo key obtained from scan
-	 * @return - BindingSet satisfying any specified constant constraints
-	 * @throws BindingSetConversionException
-	 * @throws QueryEvaluationException
-	 */
-	private BindingSet getBindingSet(Key key)
-			throws BindingSetConversionException, QueryEvaluationException {
-		byte[] row = key.getRow().getBytes();
-		String[] varOrder = key.getColumnFamily().toString()
-				.split(ExternalTupleSet.VAR_ORDER_DELIM);
-
-		BindingSet bindingSet = converter.convert(row, new VariableOrder(
-				varOrder));
-
-		QueryBindingSet bs = new QueryBindingSet();
-		for (String var : bindingSet.getBindingNames()) {
-			String mappedVar = null;
-			if(pcjVarMap.containsKey(var)) {
-				mappedVar = pcjVarMap.get(var);
-			} else {
-				throw new QueryEvaluationException("PCJ Variable has no mapping to query variable.");
-			}
-			if (constantConstraintsExist) {
-				if (mappedVar.startsWith(ExternalTupleSet.CONST_PREFIX)
-						&& constantConstraints.containsKey(mappedVar)
-						&& !constantConstraints.get(mappedVar).equals(
-								bindingSet.getValue(var))) {
-					return EMPTY_BINDINGSET;
-				}
-			}
-
-			if (!mappedVar.startsWith(ExternalTupleSet.CONST_PREFIX)) {
-					bs.addBinding(mappedVar, bindingSet.getValue(var));
-			}
-		}
-		return bs;
-	}
-
-	/**
-	 * This method forms the cross-product between an input BindingSet and the
-	 * BindingSets contained in crossProdcutBs.
-	 *
-	 * @param bs
-	 *            - {@link BindingSet} used to form cross product with
-	 *            cross-product BindingSets
-	 * @return - Iterator over resulting cross-product
-	 */
-	private Iterator<BindingSet> getCrossProducts(BindingSet bs) {
-		Set<BindingSet> crossProducts = new HashSet<BindingSet>();
-
-		for (BindingSet bSet : crossProductBs) {
-			BindingSet prod = takeCrossProduct(bSet, bs);
-			if (prod != EMPTY_BINDINGSET) {
-				crossProducts.add(prod);
-			}
-		}
-
-		return crossProducts.iterator();
-
-	}
-
-	/**
-	 * This method compute the cross product of the BindingSet passed to the PCJ
-	 * and the PCJ BindingSet.  It verifies that only common variables are unassured
-	 * variables, and if leftBs and rightBs have distinct values for a given variable,
-	 * this method uses the value from leftBs in the cross product BindingSet - this
-	 * is effectively performing a LeftJoin.
-	 *
-	 * @param leftBs - BindingSet passed to PCJ
-	 * @param rightBs - PCJ BindingSet
-	 * @return - cross product BindingSet
-	 */
-	private BindingSet takeCrossProduct(BindingSet leftBs, BindingSet rightBs) {
-		if (bindingSetsIntersect(leftBs, rightBs)) {
-			return EMPTY_BINDINGSET;
-		}
-		QueryBindingSet bs = new QueryBindingSet(leftBs);
-
-		//only add Bindings corresponding to variables that have no value
-		//assigned.  This takes into account case where leftBs and rightBs
-		//share a common, unAssuredVariable.  In this case, use value corresponding
-		//to leftBs, which is effectively performing a LeftJoin.
-		for(String s: rightBs.getBindingNames()) {
-			if(bs.getValue(s) == null) {
-				bs.addBinding(s, rightBs.getValue(s));
-			}
-		}
-		return bs;
-	}
-
-	private boolean bindingSetsIntersect(BindingSet bs1, BindingSet bs2) {
-
-		for(String s: bs1.getBindingNames()) {
-			if(bs2.getValue(s) != null && !unAssuredVariables.contains(s)) {
-				return true;
-			}
-		}
-		return false;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/accumulo/pcj/iterators/PCJKeyToJoinBindingSetIterator.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/accumulo/pcj/iterators/PCJKeyToJoinBindingSetIterator.java b/extras/indexing/src/main/java/mvm/rya/accumulo/pcj/iterators/PCJKeyToJoinBindingSetIterator.java
deleted file mode 100644
index 1b821d4..0000000
--- a/extras/indexing/src/main/java/mvm/rya/accumulo/pcj/iterators/PCJKeyToJoinBindingSetIterator.java
+++ /dev/null
@@ -1,199 +0,0 @@
-package mvm.rya.accumulo.pcj.iterators;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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.
- */
-
-import info.aduna.iteration.CloseableIteration;
-
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.NoSuchElementException;
-
-import mvm.rya.api.RdfCloudTripleStoreUtils;
-import mvm.rya.indexing.external.tupleSet.ExternalTupleSet;
-
-import org.apache.accumulo.core.client.BatchScanner;
-import org.apache.accumulo.core.client.Scanner;
-import org.apache.accumulo.core.data.Key;
-import org.apache.rya.indexing.pcj.storage.accumulo.AccumuloPcjSerializer;
-import org.apache.rya.indexing.pcj.storage.accumulo.BindingSetConverter.BindingSetConversionException;
-import org.apache.rya.indexing.pcj.storage.accumulo.VariableOrder;
-import org.openrdf.model.Value;
-import org.openrdf.query.BindingSet;
-import org.openrdf.query.QueryEvaluationException;
-import org.openrdf.query.algebra.evaluation.QueryBindingSet;
-
-import com.google.common.base.Preconditions;
-import com.google.common.collect.HashBiMap;
-
-/**
- * This class takes in a {@link Scanner} and a Collection of BindingSets,
- * deserializes each {@link Map.Entry<Key,Value>} taken from the Scanner into a
- * {@link BindingSet}, and creates a {@link Map.Entry<String, BindingSet>}
- * object to perform as hash join. The user can also specify a {@link Map
- * <String, Value>} of constant constraints that can be used to filter.
- *
- */
-public class PCJKeyToJoinBindingSetIterator
-		implements
-		CloseableIteration<Map.Entry<String, BindingSet>, QueryEvaluationException> {
-
-	//map of variables as they appear in PCJ table to query variables
-	private Map<String, String> pcjVarMap;
-	//constant constraints used for filtering
-	private Map<String, Value> constantConstraints;
-	//max number of variables an entry in the batch of BindingSets had in common with PCJ
-	//this is used for constructing hash join key.
-	private int maxPrefixLen;
-	private static final AccumuloPcjSerializer converter = new AccumuloPcjSerializer();
-	private final Map.Entry<String, BindingSet> EMPTY_ENTRY = new RdfCloudTripleStoreUtils.CustomEntry<String, BindingSet>(
-			"", new QueryBindingSet());
-	private Iterator<Entry<Key, org.apache.accumulo.core.data.Value>> iterator;
-	private boolean hasNextCalled = false;
-	private boolean isEmpty = false;
-	private Map.Entry<String, BindingSet> next;
-	private BatchScanner scanner;
-
-	public PCJKeyToJoinBindingSetIterator(BatchScanner scanner,
-			Map<String, String> pcjVarMap,
-			Map<String, Value> constantConstraints, int maxPrefixLen) {
-		Preconditions.checkNotNull(scanner);
-		Preconditions.checkArgument(pcjVarMap.size() > 0,
-				"Variable map must contain at least one variable!");
-		Preconditions.checkNotNull(constantConstraints,
-				"Constant constraints cannot be null.");
-		Preconditions.checkArgument(maxPrefixLen > 0,
-				"Max prefix length must be greater than 0.");
-		Preconditions
-				.checkArgument(maxPrefixLen <= pcjVarMap.size(),
-						"Max prefix length must be less than total number of binding names.");
-		this.scanner = scanner;
-		this.pcjVarMap = HashBiMap.create(pcjVarMap).inverse();
-		this.constantConstraints = constantConstraints;
-		this.maxPrefixLen = maxPrefixLen;
-		this.iterator = scanner.iterator();
-
-	}
-
-	public PCJKeyToJoinBindingSetIterator(BatchScanner scanner,
-			Map<String, String> pcjVarMap, int maxPrefixLen) {
-		this(scanner, pcjVarMap, new HashMap<String, Value>(), maxPrefixLen);
-	}
-
-	@Override
-	public boolean hasNext() throws QueryEvaluationException {
-
-		if (!hasNextCalled && !isEmpty) {
-			while (iterator.hasNext()) {
-				Key key = iterator.next().getKey();
-				// get bindings from scan without values associated with
-				// constant constraints
-				try {
-					next = getBindingSetEntryAndMatchConstants(key);
-				} catch (BindingSetConversionException e) {
-					throw new QueryEvaluationException(
-							"Could not deserialize PCJ BindingSet.");
-				}
-				// skip key if constant constraint don't match
-				if (next == EMPTY_ENTRY) {
-					continue;
-				}
-				hasNextCalled = true;
-				return true;
-			}
-			isEmpty = true;
-			return false;
-		} else if (isEmpty) {
-			return false;
-		} else {
-			return true;
-		}
-	}
-
-	@Override
-	public Entry<String, BindingSet> next() throws QueryEvaluationException {
-		if (hasNextCalled) {
-			hasNextCalled = false;
-		} else if (isEmpty) {
-			throw new NoSuchElementException();
-		} else {
-			if (this.hasNext()) {
-				hasNextCalled = false;
-			} else {
-				throw new NoSuchElementException();
-			}
-		}
-		return next;
-	}
-
-	@Override
-	public void remove() throws QueryEvaluationException {
-		throw new UnsupportedOperationException();
-	}
-
-	@Override
-	public void close() throws QueryEvaluationException {
-		scanner.close();
-	}
-
-	/**
-	 *
-	 * @param key
-	 *            - Accumulo key obtained from scan
-	 * @return - Entry<String,BindingSet> satisfying the constant constraints
-	 * @throws BindingSetConversionException
-	 */
-	private Map.Entry<String, BindingSet> getBindingSetEntryAndMatchConstants(
-			Key key) throws BindingSetConversionException {
-		byte[] row = key.getRow().getBytes();
-		String[] varOrder = key.getColumnFamily().toString()
-				.split(ExternalTupleSet.VAR_ORDER_DELIM);
-
-		BindingSet bindingSet = converter.convert(row, new VariableOrder(
-				varOrder));
-
-		QueryBindingSet bs = new QueryBindingSet();
-		for (String var : bindingSet.getBindingNames()) {
-			String mappedVar = pcjVarMap.get(var);
-			if (mappedVar.startsWith(ExternalTupleSet.CONST_PREFIX)
-					&& constantConstraints.containsKey(mappedVar)
-					&& !constantConstraints.get(mappedVar).equals(
-							bindingSet.getValue(var))) {
-				return EMPTY_ENTRY;
-			} else {
-				bs.addBinding(mappedVar, bindingSet.getValue(var));
-			}
-		}
-
-		String orderedValueString = bindingSet.getValue(varOrder[0]).toString();
-		for (int i = 1; i < maxPrefixLen; i++) {
-			Value value = bindingSet.getValue(varOrder[i]);
-			if (value != null) {
-				orderedValueString = orderedValueString
-						+ ExternalTupleSet.VALUE_DELIM + value.toString();
-			}
-		}
-
-		return new RdfCloudTripleStoreUtils.CustomEntry<String, BindingSet>(
-				orderedValueString, bs);
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloBatchUpdatePCJ.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloBatchUpdatePCJ.java b/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloBatchUpdatePCJ.java
deleted file mode 100644
index 53f29f4..0000000
--- a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloBatchUpdatePCJ.java
+++ /dev/null
@@ -1,244 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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 mvm.rya.api.client.accumulo;
-
-import static java.util.Objects.requireNonNull;
-
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-
-import org.apache.accumulo.core.client.AccumuloException;
-import org.apache.accumulo.core.client.AccumuloSecurityException;
-import org.apache.accumulo.core.client.Connector;
-import org.apache.log4j.Logger;
-import org.apache.rya.indexing.pcj.storage.PcjMetadata;
-import org.apache.rya.indexing.pcj.storage.PrecomputedJoinStorage;
-import org.apache.rya.indexing.pcj.storage.PrecomputedJoinStorage.PCJStorageException;
-import org.apache.rya.indexing.pcj.storage.accumulo.AccumuloPcjStorage;
-import org.apache.rya.indexing.pcj.storage.accumulo.VisibilityBindingSet;
-import org.openrdf.query.BindingSet;
-import org.openrdf.query.MalformedQueryException;
-import org.openrdf.query.QueryEvaluationException;
-import org.openrdf.query.parser.ParsedQuery;
-import org.openrdf.query.parser.sparql.SPARQLParser;
-import org.openrdf.sail.Sail;
-import org.openrdf.sail.SailConnection;
-import org.openrdf.sail.SailException;
-
-import com.google.common.base.Optional;
-
-import info.aduna.iteration.CloseableIteration;
-import mvm.rya.accumulo.AccumuloRdfConfiguration;
-import mvm.rya.accumulo.instance.AccumuloRyaInstanceDetailsRepository;
-import mvm.rya.api.client.BatchUpdatePCJ;
-import mvm.rya.api.client.InstanceDoesNotExistException;
-import mvm.rya.api.client.PCJDoesNotExistException;
-import mvm.rya.api.client.RyaClientException;
-import mvm.rya.api.instance.RyaDetails;
-import mvm.rya.api.instance.RyaDetails.PCJIndexDetails.PCJDetails;
-import mvm.rya.api.instance.RyaDetails.PCJIndexDetails.PCJDetails.PCJUpdateStrategy;
-import mvm.rya.api.instance.RyaDetailsRepository;
-import mvm.rya.api.instance.RyaDetailsRepository.NotInitializedException;
-import mvm.rya.api.instance.RyaDetailsRepository.RyaDetailsRepositoryException;
-import mvm.rya.api.instance.RyaDetailsUpdater;
-import mvm.rya.api.instance.RyaDetailsUpdater.RyaDetailsMutator;
-import mvm.rya.api.instance.RyaDetailsUpdater.RyaDetailsMutator.CouldNotApplyMutationException;
-import mvm.rya.api.persist.RyaDAOException;
-import mvm.rya.indexing.accumulo.ConfigUtils;
-import mvm.rya.rdftriplestore.inference.InferenceEngineException;
-import mvm.rya.sail.config.RyaSailFactory;
-
-/**
- * Uses an in memory Rya Client to batch update a PCJ index.
- */
-public class AccumuloBatchUpdatePCJ extends AccumuloCommand implements BatchUpdatePCJ {
-
-    private static final Logger log = Logger.getLogger(AccumuloBatchUpdatePCJ.class);
-
-    /**
-     * Constructs an instance of {@link AccumuloBatchUpdatePCJ}.
-     *
-     * @param connectionDetails - Details about the values that were used to create the connector to the cluster. (not null)
-     * @param connector - Provides programmatic access to the instance of Accumulo that hosts Rya instance. (not null)
-     */
-    public AccumuloBatchUpdatePCJ(final AccumuloConnectionDetails connectionDetails, final Connector connector) {
-        super(connectionDetails, connector);
-    }
-
-    @Override
-    public void batchUpdate(final String ryaInstanceName, final String pcjId) throws InstanceDoesNotExistException, PCJDoesNotExistException, RyaClientException {
-        requireNonNull(ryaInstanceName);
-        requireNonNull(pcjId);
-        verifyPCJState(ryaInstanceName, pcjId);
-        updatePCJResults(ryaInstanceName, pcjId);
-        updatePCJMetadata(ryaInstanceName, pcjId);
-    }
-
-    private void verifyPCJState(final String ryaInstanceName, final String pcjId) throws RyaClientException {
-        try {
-            // Fetch the Rya instance's details.
-            final RyaDetailsRepository detailsRepo = new AccumuloRyaInstanceDetailsRepository(super.getConnector(), ryaInstanceName);
-            final RyaDetails ryaDetails = detailsRepo.getRyaInstanceDetails();
-
-            // Ensure PCJs are enabled.
-            if(!ryaDetails.getPCJIndexDetails().isEnabled()) {
-                throw new RyaClientException("PCJs are not enabled for the Rya instance named '" + ryaInstanceName + "'.");
-            }
-
-            // Ensure the PCJ exists.
-            if(!ryaDetails.getPCJIndexDetails().getPCJDetails().containsKey(pcjId)) {
-                throw new PCJDoesNotExistException("The PCJ with id '" + pcjId + "' does not exist within Rya instance '" + ryaInstanceName + "'.");
-            }
-
-            // Ensure the PCJ is not already being incrementally updated.
-            final PCJDetails pcjDetails = ryaDetails.getPCJIndexDetails().getPCJDetails().get(pcjId);
-            final Optional<PCJUpdateStrategy> updateStrategy = pcjDetails.getUpdateStrategy();
-            if(updateStrategy.isPresent() && updateStrategy.get() == PCJUpdateStrategy.INCREMENTAL) {
-                throw new RyaClientException("The PCJ with id '" + pcjId + "' is already being updated incrementally.");
-            }
-        } catch(final NotInitializedException e) {
-            throw new InstanceDoesNotExistException("No RyaDetails are initialized for the Rya instance named '" + ryaInstanceName + "'.", e);
-        } catch (final RyaDetailsRepositoryException e) {
-            throw new RyaClientException("Could not fetch the RyaDetails for the Rya instance named '" + ryaInstanceName + "'.", e);
-        }
-    }
-
-    private void updatePCJResults(final String ryaInstanceName, final String pcjId) throws InstanceDoesNotExistException, PCJDoesNotExistException, RyaClientException {
-        // Things that have to be closed before we exit.
-        Sail sail = null;
-        SailConnection sailConn = null;
-        CloseableIteration<? extends BindingSet, QueryEvaluationException> results = null;
-
-        try {
-            // Create an instance of Sail backed by the Rya instance.
-            sail = connectToRya(ryaInstanceName);
-
-            // Purge the old results from the PCJ.
-            final PrecomputedJoinStorage pcjStorage = new AccumuloPcjStorage(super.getConnector(), ryaInstanceName);
-            try {
-                pcjStorage.purge(pcjId);
-            } catch (final PCJStorageException e) {
-                throw new RyaClientException("Could not batch update PCJ with ID '" + pcjId + "' because the old " +
-                        "results could not be purged from it.", e);
-            }
-
-            try {
-                // Parse the PCJ's SPARQL query.
-                final PcjMetadata metadata = pcjStorage.getPcjMetadata(pcjId);
-                final String sparql = metadata.getSparql();
-                final SPARQLParser parser = new SPARQLParser();
-                final ParsedQuery parsedQuery = parser.parseQuery(sparql, null);
-
-                // Execute the query.
-                sailConn = sail.getConnection();
-                results = sailConn.evaluate(parsedQuery.getTupleExpr(), null, null, false);
-
-                // Load the results into the PCJ table.
-                final List<VisibilityBindingSet> batch = new ArrayList<>(1000);
-
-                while(results.hasNext()) {
-                    final VisibilityBindingSet result = new VisibilityBindingSet(results.next(), "");
-                    batch.add(result);
-
-                    if(batch.size() == 1000) {
-                        pcjStorage.addResults(pcjId, batch);
-                        batch.clear();
-                    }
-                }
-
-                if(!batch.isEmpty()) {
-                    pcjStorage.addResults(pcjId, batch);
-                    batch.clear();
-                }
-            } catch(final MalformedQueryException | PCJStorageException | SailException | QueryEvaluationException e) {
-                throw new RyaClientException("Fail to batch load new results into the PCJ with ID '" + pcjId + "'.", e);
-            }
-        } finally {
-            if(results != null) {
-                try {
-                    results.close();
-                } catch (final QueryEvaluationException e) {
-                    log.warn(e.getMessage(), e);
-                }
-            }
-
-            if(sailConn != null) {
-                try {
-                    sailConn.close();
-                } catch (final SailException e) {
-                    log.warn(e.getMessage(), e);
-                }
-            }
-
-            if(sail != null) {
-                try {
-                    sail.shutDown();
-                } catch (final SailException e) {
-                    log.warn(e.getMessage(), e);
-                }
-            }
-        }
-    }
-
-    private Sail connectToRya(final String ryaInstanceName) throws RyaClientException {
-        try {
-            final AccumuloConnectionDetails connectionDetails = super.getAccumuloConnectionDetails();
-
-            final AccumuloRdfConfiguration ryaConf = new AccumuloRdfConfiguration();
-            ryaConf.setTablePrefix(ryaInstanceName);
-            ryaConf.set(ConfigUtils.CLOUDBASE_USER, connectionDetails.getUsername());
-            ryaConf.set(ConfigUtils.CLOUDBASE_PASSWORD, new String(connectionDetails.getPassword()));
-            ryaConf.set(ConfigUtils.CLOUDBASE_ZOOKEEPERS, connectionDetails.getZookeepers());
-            ryaConf.set(ConfigUtils.CLOUDBASE_INSTANCE, connectionDetails.getInstanceName());
-
-            // Turn PCJs off so that we will only scan the core Rya tables while building the PCJ results.
-            ryaConf.set(ConfigUtils.USE_PCJ, "false");
-
-            return RyaSailFactory.getInstance(ryaConf);
-        } catch (SailException | AccumuloException | AccumuloSecurityException | RyaDAOException | InferenceEngineException e) {
-            throw new RyaClientException("Could not connect to the Rya instance named '" + ryaInstanceName + "'.", e);
-        }
-    }
-
-    private void updatePCJMetadata(final String ryaInstanceName, final String pcjId) throws RyaClientException {
-        // Update the PCJ's metadata to indicate it was just batch updated.
-        try {
-            final RyaDetailsRepository detailsRepo = new AccumuloRyaInstanceDetailsRepository(super.getConnector(), ryaInstanceName);
-
-            new RyaDetailsUpdater(detailsRepo).update(new RyaDetailsMutator() {
-                @Override
-                public RyaDetails mutate(final RyaDetails originalDetails) throws CouldNotApplyMutationException {
-                    // Update the original PCJ Details to indicate they were batch updated.
-                    final PCJDetails originalPCJDetails = originalDetails.getPCJIndexDetails().getPCJDetails().get(pcjId);
-                    final PCJDetails.Builder mutatedPCJDetails = PCJDetails.builder( originalPCJDetails )
-                            .setUpdateStrategy( PCJUpdateStrategy.BATCH )
-                            .setLastUpdateTime( new Date());
-
-                    // Replace the old PCJ Details with the updated ones.
-                    final RyaDetails.Builder builder = RyaDetails.builder(originalDetails);
-                    builder.getPCJIndexDetails().addPCJDetails( mutatedPCJDetails );
-                    return builder.build();
-                }
-            });
-        } catch (final RyaDetailsRepositoryException | CouldNotApplyMutationException e) {
-            throw new RyaClientException("Could not update the PCJ's metadata.", e);
-        }
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloCommand.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloCommand.java b/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloCommand.java
deleted file mode 100644
index 078e985..0000000
--- a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloCommand.java
+++ /dev/null
@@ -1,64 +0,0 @@
-/**
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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 mvm.rya.api.client.accumulo;
-
-import static java.util.Objects.requireNonNull;
-
-import javax.annotation.ParametersAreNonnullByDefault;
-
-import org.apache.accumulo.core.client.Connector;
-
-/**
- * An abstract class that holds onto Accumulo access information. Extend this
- * when implementing a command that interacts with Accumulo.
- */
-@ParametersAreNonnullByDefault
-public abstract class AccumuloCommand {
-
-    private final AccumuloConnectionDetails connectionDetails;
-    private final Connector connector;
-
-    /**
-     * Constructs an instance of {@link AccumuloCommand}.
-     *
-     * Details about the values that were used to create the connector to the cluster. (not null)
-     * @param connector - Provides programatic access to the instance of Accumulo
-     *   that hosts Rya instance. (not null)
-     */
-    public AccumuloCommand(
-            final AccumuloConnectionDetails connectionDetails,
-            final Connector connector) {
-        this.connectionDetails = requireNonNull( connectionDetails );
-        this.connector = requireNonNull(connector);
-    }
-
-    /**
-     * @return Details about the values that were used to create the connector to the cluster. (not null)
-     */
-    public AccumuloConnectionDetails getAccumuloConnectionDetails() {
-        return connectionDetails;
-    }
-
-    /**
-     * @return Provides programatic access to the instance of Accumulo that hosts Rya instance.
-     */
-    public Connector getConnector() {
-        return connector;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloConnectionDetails.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloConnectionDetails.java b/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloConnectionDetails.java
deleted file mode 100644
index c0a7be7..0000000
--- a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloConnectionDetails.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/**
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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 mvm.rya.api.client.accumulo;
-
-import static java.util.Objects.requireNonNull;
-
-import javax.annotation.ParametersAreNonnullByDefault;
-import javax.annotation.concurrent.Immutable;
-
-/**
- * The information that the shell used to connect to Accumulo.
- */
-@Immutable
-@ParametersAreNonnullByDefault
-public class AccumuloConnectionDetails {
-    private final String username;
-    private final char[] password;
-    private final String instanceName;
-    private final String zookeepers;
-
-    /**
-     * Constructs an instance of {@link AccumuloConnectionDetails}.
-     *
-     * @param username - The username that was used to establish the connection. (not null)
-     * @param password - The password that was used to establish the connection. (not null)
-     * @param instanceName - The Accumulo instance name that was used to establish the connection. (not null)
-     * @param zookeepers - The list of zookeeper hostname that were used to establish the connection. (not null)
-     */
-    public AccumuloConnectionDetails(
-            final String username,
-            final char[] password,
-            final String instanceName,
-            final String zookeepers) {
-        this.username = requireNonNull(username);
-        this.password = requireNonNull(password);
-        this.instanceName = requireNonNull(instanceName);
-        this.zookeepers = requireNonNull(zookeepers);
-    }
-
-    /**
-     * @return The username that was used to establish the connection.
-     */
-    public String getUsername() {
-        return username;
-    }
-
-    /**
-     * @return The password that was used to establish the connection.
-     */
-    public char[] getPassword() {
-        return password;
-    }
-
-    /**
-     * @return The Accumulo instance name that was used to establish the connection.
-     */
-    public String getInstanceName() {
-        return instanceName;
-    }
-
-    /**
-     * @return The list of zookeeper hostname that were used to establish the connection.
-     */
-    public String getZookeepers() {
-        return zookeepers;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloCreatePCJ.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloCreatePCJ.java b/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloCreatePCJ.java
deleted file mode 100644
index 4cf0935..0000000
--- a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloCreatePCJ.java
+++ /dev/null
@@ -1,181 +0,0 @@
-/**
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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 mvm.rya.api.client.accumulo;
-
-import static com.google.common.base.Preconditions.checkNotNull;
-import static java.util.Objects.requireNonNull;
-
-import javax.annotation.ParametersAreNonnullByDefault;
-
-import org.apache.accumulo.core.client.Connector;
-import org.apache.rya.indexing.pcj.storage.PcjException;
-import org.apache.rya.indexing.pcj.storage.PrecomputedJoinStorage;
-import org.apache.rya.indexing.pcj.storage.PrecomputedJoinStorage.PCJStorageException;
-import org.apache.rya.indexing.pcj.storage.accumulo.AccumuloPcjStorage;
-import org.openrdf.query.MalformedQueryException;
-import org.openrdf.query.QueryEvaluationException;
-import org.openrdf.repository.RepositoryException;
-import org.openrdf.sail.SailException;
-
-import com.google.common.base.Optional;
-
-import org.apache.fluo.api.client.FluoClient;
-import mvm.rya.accumulo.AccumuloRdfConfiguration;
-import mvm.rya.accumulo.AccumuloRyaDAO;
-import mvm.rya.accumulo.instance.AccumuloRyaInstanceDetailsRepository;
-import mvm.rya.api.client.CreatePCJ;
-import mvm.rya.api.client.GetInstanceDetails;
-import mvm.rya.api.client.InstanceDoesNotExistException;
-import mvm.rya.api.client.RyaClientException;
-import mvm.rya.api.instance.RyaDetails;
-import mvm.rya.api.instance.RyaDetails.PCJIndexDetails;
-import mvm.rya.api.instance.RyaDetails.PCJIndexDetails.FluoDetails;
-import mvm.rya.api.instance.RyaDetails.PCJIndexDetails.PCJDetails;
-import mvm.rya.api.instance.RyaDetails.PCJIndexDetails.PCJDetails.PCJUpdateStrategy;
-import mvm.rya.api.instance.RyaDetailsRepository;
-import mvm.rya.api.instance.RyaDetailsRepository.RyaDetailsRepositoryException;
-import mvm.rya.api.instance.RyaDetailsUpdater;
-import mvm.rya.api.instance.RyaDetailsUpdater.RyaDetailsMutator;
-import mvm.rya.api.instance.RyaDetailsUpdater.RyaDetailsMutator.CouldNotApplyMutationException;
-import mvm.rya.rdftriplestore.RdfCloudTripleStore;
-import mvm.rya.rdftriplestore.RyaSailRepository;
-
-/**
- * An Accumulo implementation of the {@link CreatePCJ} command.
- */
-@ParametersAreNonnullByDefault
-public class AccumuloCreatePCJ extends AccumuloCommand implements CreatePCJ {
-
-    private final GetInstanceDetails getInstanceDetails;
-
-    /**
-     * Constructs an instance of {@link AccumuloCreatePCJ}.
-     *
-     * @param connectionDetails - Details about the values that were used to create the connector to the cluster. (not null)
-     * @param connector - Provides programatic access to the instance of Accumulo that hosts Rya instance. (not null)
-     */
-    public AccumuloCreatePCJ(final AccumuloConnectionDetails connectionDetails, final Connector connector) {
-        super(connectionDetails, connector);
-        getInstanceDetails = new AccumuloGetInstanceDetails(connectionDetails, connector);
-    }
-
-    @Override
-    public String createPCJ(final String instanceName, final String sparql) throws InstanceDoesNotExistException, RyaClientException {
-        requireNonNull(instanceName);
-        requireNonNull(sparql);
-
-        final Optional<RyaDetails> ryaDetailsHolder = getInstanceDetails.getDetails(instanceName);
-        final boolean ryaInstanceExists = ryaDetailsHolder.isPresent();
-        if(!ryaInstanceExists) {
-            throw new InstanceDoesNotExistException(String.format("The '%s' instance of Rya does not exist.", instanceName));
-        }
-
-        final PCJIndexDetails pcjIndexDetails = ryaDetailsHolder.get().getPCJIndexDetails();
-        final boolean pcjIndexingEnabeld = pcjIndexDetails.isEnabled();
-        if(!pcjIndexingEnabeld) {
-            throw new RyaClientException(String.format("The '%s' instance of Rya does not have PCJ Indexing enabled.", instanceName));
-        }
-
-        // Create the PCJ table that will receive the index results.
-        final String pcjId;
-        final PrecomputedJoinStorage pcjStorage = new AccumuloPcjStorage(getConnector(), instanceName);
-        try {
-            pcjId = pcjStorage.createPcj(sparql);
-        } catch (final PCJStorageException e) {
-            throw new RyaClientException("Problem while initializing the PCJ table.", e);
-        }
-
-        // If a Fluo application is being used, task it with updating the PCJ.
-        final Optional<FluoDetails> fluoDetailsHolder = pcjIndexDetails.getFluoDetails();
-        if(fluoDetailsHolder.isPresent()) {
-            final String fluoAppName = fluoDetailsHolder.get().getUpdateAppName();
-            try {
-                updateFluoApp(instanceName, fluoAppName, pcjStorage, pcjId);
-            } catch (RepositoryException | MalformedQueryException | SailException | QueryEvaluationException | PcjException e) {
-                throw new RyaClientException("Problem while initializing the Fluo application with the new PCJ.", e);
-            }
-
-            // Update the Rya Details to indicate the PCJ is being updated incrementally.
-            final RyaDetailsRepository detailsRepo = new AccumuloRyaInstanceDetailsRepository(getConnector(), instanceName);
-            try {
-                new RyaDetailsUpdater(detailsRepo).update(new RyaDetailsMutator() {
-                    @Override
-                    public RyaDetails mutate(final RyaDetails originalDetails) throws CouldNotApplyMutationException {
-                        // Update the original PCJ Details to indicate they are incrementally updated.
-                        final PCJDetails originalPCJDetails = originalDetails.getPCJIndexDetails().getPCJDetails().get(pcjId);
-                        final PCJDetails.Builder mutatedPCJDetails = PCJDetails.builder( originalPCJDetails )
-                            .setUpdateStrategy( PCJUpdateStrategy.INCREMENTAL );
-
-                        // Replace the old PCJ Details with the updated ones.
-                        final RyaDetails.Builder builder = RyaDetails.builder(originalDetails);
-                        builder.getPCJIndexDetails().addPCJDetails( mutatedPCJDetails );
-                        return builder.build();
-                    }
-                });
-            } catch (RyaDetailsRepositoryException | CouldNotApplyMutationException e) {
-                throw new RyaClientException("Problem while updating the Rya instance's Details to indicate the PCJ is being incrementally updated.", e);
-            }
-        }
-
-        // Return the ID that was assigned to the PCJ.
-        return pcjId;
-    }
-
-    private void updateFluoApp(final String ryaInstance, final String fluoAppName, final PrecomputedJoinStorage pcjStorage, final String pcjId) throws RepositoryException, MalformedQueryException, SailException, QueryEvaluationException, PcjException {
-        requireNonNull(pcjStorage);
-        requireNonNull(pcjId);
-
-        // Connect to the Fluo application that is updating this instance's PCJs.
-        final AccumuloConnectionDetails cd = super.getAccumuloConnectionDetails();
-        final FluoClient fluoClient = new FluoClientFactory().connect(
-                cd.getUsername(),
-                new String(cd.getPassword()),
-                cd.getInstanceName(),
-                cd.getZookeepers(),
-                fluoAppName);
-
-        // Setup the Rya client that is able to talk to scan Rya's statements.
-        final RyaSailRepository ryaSailRepo = makeRyaRepository(getConnector(), ryaInstance);
-
-        // Initialize the PCJ within the Fluo application.
-        final org.apache.rya.indexing.pcj.fluo.api.CreatePcj fluoCreatePcj = new org.apache.rya.indexing.pcj.fluo.api.CreatePcj();
-        fluoCreatePcj.withRyaIntegration(pcjId, pcjStorage, fluoClient, ryaSailRepo);
-    }
-
-    private static RyaSailRepository makeRyaRepository(final Connector connector, final String ryaInstance) throws RepositoryException {
-        checkNotNull(connector);
-        checkNotNull(ryaInstance);
-
-        // Setup Rya configuration values.
-        final AccumuloRdfConfiguration ryaConf = new AccumuloRdfConfiguration();
-        ryaConf.setTablePrefix( ryaInstance );
-
-        // Connect to the Rya repo using the provided Connector.
-        final AccumuloRyaDAO accumuloRyaDao = new AccumuloRyaDAO();
-        accumuloRyaDao.setConnector(connector);
-        accumuloRyaDao.setConf(ryaConf);
-
-        final RdfCloudTripleStore ryaStore = new RdfCloudTripleStore();
-        ryaStore.setRyaDAO(accumuloRyaDao);
-
-        final RyaSailRepository ryaRepo = new RyaSailRepository(ryaStore);
-        ryaRepo.initialize();
-        return ryaRepo;
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloDeletePCJ.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloDeletePCJ.java b/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloDeletePCJ.java
deleted file mode 100644
index 233a265..0000000
--- a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloDeletePCJ.java
+++ /dev/null
@@ -1,130 +0,0 @@
-/**
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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 mvm.rya.api.client.accumulo;
-
-import static java.util.Objects.requireNonNull;
-
-import javax.annotation.ParametersAreNonnullByDefault;
-
-import org.apache.accumulo.core.client.Connector;
-import org.apache.rya.indexing.pcj.fluo.api.DeletePcj;
-import org.apache.rya.indexing.pcj.storage.PrecomputedJoinStorage;
-import org.apache.rya.indexing.pcj.storage.PrecomputedJoinStorage.PCJStorageException;
-import org.apache.rya.indexing.pcj.storage.accumulo.AccumuloPcjStorage;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.google.common.base.Optional;
-
-import org.apache.fluo.api.client.FluoClient;
-import mvm.rya.api.client.DeletePCJ;
-import mvm.rya.api.client.GetInstanceDetails;
-import mvm.rya.api.client.InstanceDoesNotExistException;
-import mvm.rya.api.client.RyaClientException;
-import mvm.rya.api.instance.RyaDetails;
-import mvm.rya.api.instance.RyaDetails.PCJIndexDetails;
-import mvm.rya.api.instance.RyaDetails.PCJIndexDetails.FluoDetails;
-import mvm.rya.api.instance.RyaDetails.PCJIndexDetails.PCJDetails;
-import mvm.rya.api.instance.RyaDetails.PCJIndexDetails.PCJDetails.PCJUpdateStrategy;
-
-/**
- * An Accumulo implementation of the {@link DeletePCJ} command.
- */
-@ParametersAreNonnullByDefault
-public class AccumuloDeletePCJ extends AccumuloCommand implements DeletePCJ {
-
-    private static final Logger log = LoggerFactory.getLogger(AccumuloDeletePCJ.class);
-
-    private final GetInstanceDetails getInstanceDetails;
-
-    /**
-     * Constructs an instance of {@link AccumuloDeletePCJ}.
-     *
-     * @param connectionDetails - Details about the values that were used to create the connector to the cluster. (not null)
-     * @param connector - Provides programatic access to the instance of Accumulo that hosts Rya instance. (not null)
-     */
-    public AccumuloDeletePCJ(final AccumuloConnectionDetails connectionDetails, final Connector connector) {
-        super(connectionDetails, connector);
-        getInstanceDetails = new AccumuloGetInstanceDetails(connectionDetails, connector);
-    }
-
-    @Override
-    public void deletePCJ(final String instanceName, final String pcjId) throws InstanceDoesNotExistException, RyaClientException {
-        requireNonNull(instanceName);
-        requireNonNull(pcjId);
-
-        final Optional<RyaDetails> originalDetails = getInstanceDetails.getDetails(instanceName);
-        final boolean ryaInstanceExists = originalDetails.isPresent();
-        if(!ryaInstanceExists) {
-            throw new InstanceDoesNotExistException(String.format("The '%s' instance of Rya does not exist.", instanceName));
-        }
-
-        final boolean pcjIndexingEnabeld = originalDetails.get().getPCJIndexDetails().isEnabled();
-        if(!pcjIndexingEnabeld) {
-            throw new RyaClientException(String.format("The '%s' instance of Rya does not have PCJ Indexing enabled.", instanceName));
-        }
-
-        final boolean pcjExists = originalDetails.get().getPCJIndexDetails().getPCJDetails().containsKey( pcjId );
-        if(!pcjExists) {
-            throw new RyaClientException(String.format("The '%s' instance of Rya does not have PCJ with ID '%s'.", instanceName, pcjId));
-        }
-
-        // If the PCJ was being maintained by a Fluo application, then stop that process.
-        final PCJIndexDetails pcjIndexDetails  = originalDetails.get().getPCJIndexDetails();
-        final PCJDetails droppedPcjDetails = pcjIndexDetails.getPCJDetails().get( pcjId );
-        if(droppedPcjDetails.getUpdateStrategy().isPresent()) {
-            if(droppedPcjDetails.getUpdateStrategy().get() == PCJUpdateStrategy.INCREMENTAL) {
-                final Optional<FluoDetails> fluoDetailsHolder = pcjIndexDetails.getFluoDetails();
-
-                if(fluoDetailsHolder.isPresent()) {
-                    final String fluoAppName = pcjIndexDetails.getFluoDetails().get().getUpdateAppName();
-                    stopUpdatingPCJ(fluoAppName, pcjId);
-                } else {
-                    log.error(String.format("Could not stop the Fluo application from updating the PCJ because the Fluo Details are " +
-                            "missing for the Rya instance named '%s'.", instanceName));
-                }
-            }
-        }
-
-        // Drop the table that holds the PCJ results from Accumulo.
-        final PrecomputedJoinStorage pcjs = new AccumuloPcjStorage(getConnector(), instanceName);
-        try {
-            pcjs.dropPcj(pcjId);
-        } catch (final PCJStorageException e) {
-            throw new RyaClientException("Could not drop the PCJ's table from Accumulo.", e);
-        }
-    }
-
-    private void stopUpdatingPCJ(final String fluoAppName, final String pcjId) {
-        requireNonNull(fluoAppName);
-        requireNonNull(pcjId);
-
-        // Connect to the Fluo application that is updating this instance's PCJs.
-        final AccumuloConnectionDetails cd = super.getAccumuloConnectionDetails();
-        final FluoClient fluoClient = new FluoClientFactory().connect(
-                cd.getUsername(),
-                new String(cd.getPassword()),
-                cd.getInstanceName(),
-                cd.getZookeepers(),
-                fluoAppName);
-
-        // Delete the PCJ from the Fluo App.
-        new DeletePcj(1000).deletePcj(fluoClient, pcjId);
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloGetInstanceDetails.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloGetInstanceDetails.java b/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloGetInstanceDetails.java
deleted file mode 100644
index a2fed78..0000000
--- a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloGetInstanceDetails.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/**
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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 mvm.rya.api.client.accumulo;
-
-import static java.util.Objects.requireNonNull;
-
-import javax.annotation.ParametersAreNonnullByDefault;
-
-import org.apache.accumulo.core.client.Connector;
-
-import com.google.common.base.Optional;
-
-import mvm.rya.accumulo.instance.AccumuloRyaInstanceDetailsRepository;
-import mvm.rya.api.client.GetInstanceDetails;
-import mvm.rya.api.client.InstanceDoesNotExistException;
-import mvm.rya.api.client.InstanceExists;
-import mvm.rya.api.client.RyaClientException;
-import mvm.rya.api.instance.RyaDetails;
-import mvm.rya.api.instance.RyaDetailsRepository;
-import mvm.rya.api.instance.RyaDetailsRepository.NotInitializedException;
-import mvm.rya.api.instance.RyaDetailsRepository.RyaDetailsRepositoryException;
-
-/**
- * An Accumulo implementation of the {@link GetInstanceDetails} command.
- */
-@ParametersAreNonnullByDefault
-public class AccumuloGetInstanceDetails extends AccumuloCommand implements GetInstanceDetails {
-
-    private final InstanceExists instanceExists;
-
-    /**
-     * Constructs an instance of {@link AccumuloGetInstanceDetails}.
-     *
-     * @param connectionDetails - Details about the values that were used to create the connector to the cluster. (not null)
-     * @param connector - Provides programatic access to the instance of Accumulo that hosts Rya instance. (not null)
-     */
-    public AccumuloGetInstanceDetails(final AccumuloConnectionDetails connectionDetails, final Connector connector) {
-        super(connectionDetails, connector);
-        instanceExists = new AccumuloInstanceExists(connectionDetails, connector);
-    }
-
-    @Override
-    public Optional<RyaDetails> getDetails(final String instanceName) throws InstanceDoesNotExistException, RyaClientException {
-        requireNonNull(instanceName);
-
-        // Ensure the Rya instance exists.
-        if(!instanceExists.exists(instanceName)) {
-            throw new InstanceDoesNotExistException(String.format("There is no Rya instance named '%s'.", instanceName));
-        }
-
-        // If the instance has details, then return them.
-        final RyaDetailsRepository detailsRepo = new AccumuloRyaInstanceDetailsRepository(getConnector(), instanceName);
-        try {
-            return Optional.of( detailsRepo.getRyaInstanceDetails() );
-        } catch (final NotInitializedException e) {
-            return Optional.absent();
-        } catch (final RyaDetailsRepositoryException e) {
-            throw new RyaClientException("Could not fetch the Rya instance's details.", e);
-        }
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloInstall.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloInstall.java b/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloInstall.java
deleted file mode 100644
index 08c1932..0000000
--- a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloInstall.java
+++ /dev/null
@@ -1,218 +0,0 @@
-/**
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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 mvm.rya.api.client.accumulo;
-
-import static java.util.Objects.requireNonNull;
-
-import java.util.Date;
-
-import javax.annotation.ParametersAreNonnullByDefault;
-
-import org.apache.accumulo.core.client.AccumuloException;
-import org.apache.accumulo.core.client.AccumuloSecurityException;
-import org.apache.accumulo.core.client.Connector;
-import org.openrdf.sail.Sail;
-import org.openrdf.sail.SailException;
-
-import com.google.common.base.Optional;
-
-import mvm.rya.accumulo.AccumuloRdfConfiguration;
-import mvm.rya.accumulo.instance.AccumuloRyaInstanceDetailsRepository;
-import mvm.rya.api.client.Install;
-import mvm.rya.api.client.InstanceExists;
-import mvm.rya.api.client.RyaClientException;
-import mvm.rya.api.instance.RyaDetails;
-import mvm.rya.api.instance.RyaDetails.EntityCentricIndexDetails;
-import mvm.rya.api.instance.RyaDetails.FreeTextIndexDetails;
-import mvm.rya.api.instance.RyaDetails.GeoIndexDetails;
-import mvm.rya.api.instance.RyaDetails.JoinSelectivityDetails;
-import mvm.rya.api.instance.RyaDetails.PCJIndexDetails;
-import mvm.rya.api.instance.RyaDetails.PCJIndexDetails.FluoDetails;
-import mvm.rya.api.instance.RyaDetails.ProspectorDetails;
-import mvm.rya.api.instance.RyaDetails.TemporalIndexDetails;
-import mvm.rya.api.instance.RyaDetailsRepository;
-import mvm.rya.api.instance.RyaDetailsRepository.AlreadyInitializedException;
-import mvm.rya.api.instance.RyaDetailsRepository.RyaDetailsRepositoryException;
-import mvm.rya.api.persist.RyaDAOException;
-import mvm.rya.indexing.accumulo.ConfigUtils;
-import mvm.rya.indexing.external.PrecomputedJoinIndexerConfig.PrecomputedJoinStorageType;
-import mvm.rya.indexing.external.PrecomputedJoinIndexerConfig.PrecomputedJoinUpdaterType;
-import mvm.rya.rdftriplestore.inference.InferenceEngineException;
-import mvm.rya.sail.config.RyaSailFactory;
-
-/**
- * An Accumulo implementation of the {@link Install} command.
- */
-
-@ParametersAreNonnullByDefault
-public class AccumuloInstall extends AccumuloCommand implements Install {
-
-    private final InstanceExists instanceExists;
-
-    /**
-     * Constructs an instance of {@link AccumuloInstall}.
-     *
-     * @param connectionDetails - Details about the values that were used to create the connector to the cluster. (not null)
-     * @param connector - Provides programatic access to the instance of Accumulo that hosts Rya instance. (not null)
-     */
-    public AccumuloInstall(final AccumuloConnectionDetails connectionDetails, final Connector connector) {
-        super(connectionDetails, connector);
-        instanceExists = new AccumuloInstanceExists(connectionDetails, connector);
-    }
-
-    @Override
-    public void install(final String instanceName, final InstallConfiguration installConfig) throws DuplicateInstanceNameException, RyaClientException {
-        requireNonNull(instanceName);
-        requireNonNull(installConfig);
-
-        // Check to see if a Rya instance has already been installed with this name.
-        if(instanceExists.exists(instanceName)) {
-            throw new DuplicateInstanceNameException("An instance of Rya has already been installed to this Rya storage " +
-                    "with the name '" + instanceName + "'. Try again with a different name.");
-        }
-
-        // Initialize the Rya Details table.
-        RyaDetails details;
-        try {
-            details = initializeRyaDetails(instanceName, installConfig);
-        } catch (final AlreadyInitializedException e) {
-            // This can only happen if somebody else installs an instance of Rya with the name between the check and now.
-            throw new DuplicateInstanceNameException("An instance of Rya has already been installed to this Rya storage " +
-                    "with the name '" + instanceName + "'. Try again with a different name.");
-        } catch (final RyaDetailsRepositoryException e) {
-            throw new RyaClientException("The RyaDetails couldn't be initialized. Details: " + e.getMessage(), e);
-        }
-
-        // Initialize the rest of the tables used by the Rya instance.
-        final AccumuloRdfConfiguration ryaConfig = makeRyaConfig(getAccumuloConnectionDetails(), details);
-        try {
-            final Sail ryaSail = RyaSailFactory.getInstance(ryaConfig);
-            ryaSail.shutDown();
-        } catch (final AccumuloException | AccumuloSecurityException | RyaDAOException | InferenceEngineException e) {
-            throw new RyaClientException("Could not initialize all of the tables for the new Rya instance. " +
-                    "This instance may be left in a bad state.", e);
-        } catch (final SailException e) {
-            throw new RyaClientException("Problem shutting down the Sail object used to install Rya.", e);
-        }
-    }
-
-    /**
-     * @return The version of the application as reported by the manifest.
-     */
-    private String getVersion() {
-        return "" + this.getClass().getPackage().getImplementationVersion();
-    }
-
-    /**
-     * Initializes the {@link RyaDetails} and stores them for the new instance.
-     *
-     * @param instanceName - The name of the instance that is being created. (not null)
-     * @param installConfig - The instance's install configuration. (not null)
-     * @return The {@link RyaDetails} that were stored.
-     * @throws AlreadyInitializedException Could not be initialized because
-     *   a table with this instance name has already exists and is holding the details.
-     * @throws RyaDetailsRepositoryException Something caused the initialization
-     *   operation to fail.
-     */
-    private RyaDetails initializeRyaDetails(final String instanceName, final InstallConfiguration installConfig)
-            throws AlreadyInitializedException, RyaDetailsRepositoryException {
-        final RyaDetailsRepository detailsRepo = new AccumuloRyaInstanceDetailsRepository(getConnector(), instanceName);
-
-        // Build the PCJ Index details.
-        final PCJIndexDetails.Builder pcjDetailsBuilder = PCJIndexDetails.builder()
-                .setEnabled(installConfig.isPcjIndexEnabled());
-        if(installConfig.getFluoPcjAppName().isPresent()) {
-            final String fluoPcjAppName = installConfig.getFluoPcjAppName().get();
-            pcjDetailsBuilder.setFluoDetails(new FluoDetails( fluoPcjAppName ));
-        }
-
-        final RyaDetails details = RyaDetails.builder()
-                // General Metadata
-                .setRyaInstanceName(instanceName)
-                .setRyaVersion( getVersion() )
-
-                // Secondary Index Values
-                .setGeoIndexDetails(
-                        new GeoIndexDetails(installConfig.isGeoIndexEnabled()))
-                .setTemporalIndexDetails(
-                        new TemporalIndexDetails(installConfig.isTemporalIndexEnabled()))
-                .setFreeTextDetails(
-                        new FreeTextIndexDetails(installConfig.isFreeTextIndexEnabled()))
-                .setEntityCentricIndexDetails(
-                        new EntityCentricIndexDetails(installConfig.isEntityCentrixIndexEnabled()))
-                .setPCJIndexDetails(  pcjDetailsBuilder )
-
-                // Statistics values.
-                .setProspectorDetails(
-                        new ProspectorDetails(Optional.<Date>absent()) )
-                .setJoinSelectivityDetails(
-                        new JoinSelectivityDetails(Optional.<Date>absent()) )
-                .build();
-
-        // Initialize the table.
-        detailsRepo.initialize(details);
-
-        return details;
-    }
-
-    /**
-     * Builds a {@link AccumuloRdfConfiguration} object that will be used by the
-     * Rya DAO to initialize all of the tables it will need.
-     *
-     * @param connectionDetails - Indicates how to connect to Accumulo. (not null)
-     * @param details - Indicates what needs to be installed. (not null)
-     * @return A Rya Configuration object that can be used to perform the install.
-     */
-    private static AccumuloRdfConfiguration makeRyaConfig(final AccumuloConnectionDetails connectionDetails, final RyaDetails details) {
-        final AccumuloRdfConfiguration conf = new AccumuloRdfConfiguration();
-
-        // The Rya Instance Name is used as a prefix for the index tables in Accumulo.
-        conf.setTablePrefix( details.getRyaInstanceName() );
-
-        // Enable the indexers that the instance is configured to use.
-        // TODO fix me, not sure why the install command is here.
-//        conf.set(ConfigUtils.USE_GEO, "" + details.getGeoIndexDetails().isEnabled() );
-        conf.set(ConfigUtils.USE_FREETEXT, "" + details.getFreeTextIndexDetails().isEnabled() );
-        conf.set(ConfigUtils.USE_TEMPORAL, "" + details.getTemporalIndexDetails().isEnabled() );
-        conf.set(ConfigUtils.USE_ENTITY, "" + details.getEntityCentricIndexDetails().isEnabled());
-
-        conf.set(ConfigUtils.USE_PCJ, "" + details.getPCJIndexDetails().isEnabled() );
-        conf.set(ConfigUtils.PCJ_STORAGE_TYPE, PrecomputedJoinStorageType.ACCUMULO.toString());
-
-        final Optional<FluoDetails> fluoHolder = details.getPCJIndexDetails().getFluoDetails();
-        final PrecomputedJoinUpdaterType updaterType = fluoHolder.isPresent() ? PrecomputedJoinUpdaterType.FLUO : PrecomputedJoinUpdaterType.NO_UPDATE;
-        conf.set(ConfigUtils.PCJ_UPDATER_TYPE, updaterType.toString());
-
-        // XXX The Accumulo implementation of the secondary indices make need all
-        //     of the accumulo connector's parameters to initialize themselves, so
-        //     we need to include them here. It would be nice if the secondary
-        //     indexers used the connector that is provided to them instead of
-        //     building a new one.
-        conf.set(ConfigUtils.CLOUDBASE_USER, connectionDetails.getUsername());
-        conf.set(ConfigUtils.CLOUDBASE_PASSWORD, new String(connectionDetails.getPassword()));
-        conf.set(ConfigUtils.CLOUDBASE_INSTANCE, connectionDetails.getInstanceName());
-        conf.set(ConfigUtils.CLOUDBASE_ZOOKEEPERS, connectionDetails.getZookeepers());
-
-        // This initializes the living indexers that will be used by the application and
-        // caches them within the configuration object so that they may be used later.
-        ConfigUtils.setIndexers(conf);
-
-        return conf;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloInstanceExists.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloInstanceExists.java b/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloInstanceExists.java
deleted file mode 100644
index 1be7cd8..0000000
--- a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloInstanceExists.java
+++ /dev/null
@@ -1,71 +0,0 @@
-/**
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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 mvm.rya.api.client.accumulo;
-
-import static java.util.Objects.requireNonNull;
-
-import javax.annotation.ParametersAreNonnullByDefault;
-
-import org.apache.accumulo.core.client.Connector;
-import org.apache.accumulo.core.client.admin.TableOperations;
-
-import mvm.rya.accumulo.instance.AccumuloRyaInstanceDetailsRepository;
-import mvm.rya.api.RdfCloudTripleStoreConstants;
-import mvm.rya.api.client.InstanceExists;
-import mvm.rya.api.client.RyaClientException;
-
-/**
- * An Accumulo implementation of the {@link InstanceExists} command.
- */
-@ParametersAreNonnullByDefault
-public class AccumuloInstanceExists extends AccumuloCommand implements InstanceExists {
-
-    /**
-     * Constructs an insatnce of {@link AccumuloInstanceExists}.
-     *
-     * @param connectionDetails - Details about the values that were used to create the connector to the cluster. (not null)
-     * @param connector - Provides programatic access to the instance of Accumulo that hosts Rya instance. (not null)
-     */
-    public AccumuloInstanceExists(final AccumuloConnectionDetails connectionDetails, final Connector connector) {
-        super(connectionDetails, connector);
-    }
-
-    @Override
-    public boolean exists(final String instanceName) throws RyaClientException {
-        requireNonNull( instanceName );
-
-        final TableOperations tableOps = getConnector().tableOperations();
-
-        // Newer versions of Rya will have a Rya Details table.
-        final String ryaDetailsTableName = instanceName + AccumuloRyaInstanceDetailsRepository.INSTANCE_DETAILS_TABLE_NAME;
-        if(tableOps.exists(ryaDetailsTableName)) {
-            return true;
-        }
-
-        // However, older versions only have the data tables.
-        final String spoTableName = instanceName + RdfCloudTripleStoreConstants.TBL_SPO_SUFFIX;
-        final String posTableName = instanceName + RdfCloudTripleStoreConstants.TBL_PO_SUFFIX;
-        final String ospTableName = instanceName + RdfCloudTripleStoreConstants.TBL_OSP_SUFFIX;
-        if(tableOps.exists(spoTableName) && tableOps.exists(posTableName) && tableOps.exists(ospTableName)) {
-            return true;
-        }
-
-        return false;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloListInstances.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloListInstances.java b/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloListInstances.java
deleted file mode 100644
index 86d96b8..0000000
--- a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloListInstances.java
+++ /dev/null
@@ -1,141 +0,0 @@
-/**
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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 mvm.rya.api.client.accumulo;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.annotation.ParametersAreNonnullByDefault;
-
-import org.apache.accumulo.core.client.Connector;
-
-import mvm.rya.api.RdfCloudTripleStoreConstants;
-import mvm.rya.api.client.ListInstances;
-import mvm.rya.api.client.RyaClientException;
-
-/**
- * An Accumulo implementation of the {@link ListInstances} command.
- */
-@ParametersAreNonnullByDefault
-public class AccumuloListInstances extends AccumuloCommand implements ListInstances {
-
-    private final Pattern spoPattern = Pattern.compile("(.*)" + RdfCloudTripleStoreConstants.TBL_SPO_SUFFIX);
-    private final Pattern ospPattern = Pattern.compile("(.*)" + RdfCloudTripleStoreConstants.TBL_OSP_SUFFIX);
-    private final Pattern poPattern = Pattern.compile("(.*)" + RdfCloudTripleStoreConstants.TBL_PO_SUFFIX);
-
-    /**
-     * Constructs an instance of {@link AccumuloListInstances}.
-     *
-     * @param connectionDetails - Details about the values that were used to create the connector to the cluster. (not null)
-     * @param connector - Provides programatic access to the instance of Accumulo that hosts Rya instance. (not null)
-     */
-    public AccumuloListInstances(final AccumuloConnectionDetails connectionDetails, final Connector connector) {
-        super(connectionDetails, connector);
-    }
-
-    @Override
-    public List<String> listInstances() throws RyaClientException {
-        // Figure out what the instance names might be.
-        final Map<String, InstanceTablesFound> proposedInstanceNames = new HashMap<>();
-
-        for(final String table : getConnector().tableOperations().list()) {
-            // SPO table
-            final Matcher spoMatcher = spoPattern.matcher(table);
-            if(spoMatcher.find()) {
-                final String instanceName = spoMatcher.group(1);
-                makeOrGetInstanceTables(proposedInstanceNames, instanceName).setSpoFound();
-            }
-
-            // OSP table
-            final Matcher ospMatcher = ospPattern.matcher(table);
-            if(ospMatcher.find()) {
-                final String instanceName = ospMatcher.group(1);
-                makeOrGetInstanceTables(proposedInstanceNames, instanceName).setOspFound();
-            }
-
-            // PO table
-            final Matcher poMatcher = poPattern.matcher(table);
-            if(poMatcher.find()) {
-                final String instanceName = poMatcher.group(1);
-                makeOrGetInstanceTables(proposedInstanceNames, instanceName).setPoFound();
-            }
-        }
-
-        // Determine which of the proposed names fit the expected Rya table structures.
-        final List<String> instanceNames = new ArrayList<>();
-        for(final Entry<String, InstanceTablesFound> entry : proposedInstanceNames.entrySet()) {
-            final InstanceTablesFound tables = entry.getValue();
-            if(tables.allFlagsSet()) {
-                instanceNames.add(entry.getKey());
-            }
-        }
-
-        return instanceNames;
-    }
-
-    private InstanceTablesFound makeOrGetInstanceTables(final Map<String, InstanceTablesFound> lookup, final String instanceName) {
-        if(!lookup.containsKey(instanceName)) {
-            lookup.put(instanceName, new InstanceTablesFound());
-        }
-        return lookup.get(instanceName);
-    }
-
-    /**
-     * Flags that are used to determine if a String is a Rya Instance name.
-     */
-    @ParametersAreNonnullByDefault
-    private static class InstanceTablesFound {
-        private boolean spoFound = false;
-        private boolean ospFound = false;
-        private boolean poFound = false;
-
-        /**
-         * Sets the SPO table as seen.
-         */
-        public void setSpoFound() {
-            spoFound = true;
-        }
-
-        /**
-         * Sets the OSP table as seen.
-         */
-        public void setOspFound() {
-            ospFound = true;
-        }
-
-        /**
-         * Sets the POS table as seen.
-         */
-        public void setPoFound() {
-            poFound = true;
-        }
-
-        /**
-         * @return {@code true} if all of the flags have been set; otherwise {@code false}.
-         */
-        public boolean allFlagsSet() {
-            return spoFound && ospFound && poFound;
-        }
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloRyaClientFactory.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloRyaClientFactory.java b/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloRyaClientFactory.java
deleted file mode 100644
index 102f667..0000000
--- a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/AccumuloRyaClientFactory.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/**
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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 mvm.rya.api.client.accumulo;
-
-import static java.util.Objects.requireNonNull;
-
-import javax.annotation.ParametersAreNonnullByDefault;
-
-import org.apache.accumulo.core.client.Connector;
-
-import mvm.rya.api.client.RyaClient;
-
-/**
- * Constructs instance of {@link RyaClient} that are connected to instance of
- * Rya hosted by Accumulo clusters.
- */
-@ParametersAreNonnullByDefault
-public class AccumuloRyaClientFactory {
-
-    /**
-     * Initialize a set of {@link RyaClient} that will interact with an instance of
-     * Rya that is hosted by an Accumulo cluster.
-     *
-     * @param connectionDetails - Details about the values that were used to create the connector to the cluster. (not null)
-     * @param connector - The Accumulo connector the commands will use. (not null)
-     * @return The initialized commands.
-     */
-    public static RyaClient build(
-            final AccumuloConnectionDetails connectionDetails,
-            final Connector connector) {
-        requireNonNull(connectionDetails);
-        requireNonNull(connector);
-
-        // Build the RyaCommands option with the initialized commands.
-        return new RyaClient(
-                new AccumuloInstall(connectionDetails, connector),
-                new AccumuloCreatePCJ(connectionDetails, connector),
-                new AccumuloDeletePCJ(connectionDetails, connector),
-                new AccumuloBatchUpdatePCJ(connectionDetails, connector),
-                new AccumuloGetInstanceDetails(connectionDetails, connector),
-                new AccumuloInstanceExists(connectionDetails, connector),
-                new AccumuloListInstances(connectionDetails, connector));
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/FluoClientFactory.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/FluoClientFactory.java b/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/FluoClientFactory.java
deleted file mode 100644
index 0c6c2f1..0000000
--- a/extras/indexing/src/main/java/mvm/rya/api/client/accumulo/FluoClientFactory.java
+++ /dev/null
@@ -1,72 +0,0 @@
-/**
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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 mvm.rya.api.client.accumulo;
-
-import static java.util.Objects.requireNonNull;
-
-import javax.annotation.ParametersAreNonnullByDefault;
-
-import org.apache.fluo.api.client.FluoClient;
-import org.apache.fluo.api.client.FluoFactory;
-import org.apache.fluo.api.config.FluoConfiguration;
-
-/**
- * Creates {@link FluoClient}s that are connected to a specific Fluo Application.
- */
-@ParametersAreNonnullByDefault
-public class FluoClientFactory {
-
-    /**
-     * Create a {@link FluoClient} that uses the provided connection details.
-     *
-     * @param username - The username the connection will use. (not null)
-     * @param password - The password the connection will use. (not null)
-     * @param instanceName - The name of the Accumulo instance. (not null)
-     * @param zookeeperHostnames - A comma delimited list of the Zookeeper server hostnames. (not null)
-     * @param fluoAppName - The Fluo Application the client will be connected to. (not null)
-     * @return A {@link FluoClient} that may be used to access the Fluo Application.
-     */
-    public FluoClient connect(
-            final String username,
-            final String password,
-            final String instanceName,
-            final String zookeeperHostnames,
-            final String fluoAppName) {
-        requireNonNull(username);
-        requireNonNull(password);
-        requireNonNull(instanceName);
-        requireNonNull(zookeeperHostnames);
-        requireNonNull(fluoAppName);
-
-        final FluoConfiguration fluoConfig = new FluoConfiguration();
-
-        // Fluo configuration values.
-        fluoConfig.setApplicationName( fluoAppName );
-        fluoConfig.setInstanceZookeepers( zookeeperHostnames + "/fluo" );
-
-        // Accumulo Connection Stuff.
-        fluoConfig.setAccumuloZookeepers( zookeeperHostnames );
-        fluoConfig.setAccumuloInstance( instanceName );
-        fluoConfig.setAccumuloUser( username );
-        fluoConfig.setAccumuloPassword( password );
-
-        // Connect the client.
-        return FluoFactory.newClient(fluoConfig);
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/indexing/DocIdIndexer.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/indexing/DocIdIndexer.java b/extras/indexing/src/main/java/mvm/rya/indexing/DocIdIndexer.java
deleted file mode 100644
index 21d5de7..0000000
--- a/extras/indexing/src/main/java/mvm/rya/indexing/DocIdIndexer.java
+++ /dev/null
@@ -1,47 +0,0 @@
-package mvm.rya.indexing;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF 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.
- */
-
-
-import info.aduna.iteration.CloseableIteration;
-
-import java.io.Closeable;
-import java.io.IOException;
-import java.util.Collection;
-
-import mvm.rya.indexing.accumulo.entity.StarQuery;
-
-import org.apache.accumulo.core.client.TableNotFoundException;
-import org.openrdf.query.BindingSet;
-import org.openrdf.query.QueryEvaluationException;
-
-public interface DocIdIndexer extends Closeable {
-
-  
-
-    public abstract CloseableIteration<BindingSet, QueryEvaluationException> queryDocIndex(StarQuery query,
-            Collection<BindingSet> constraints) throws TableNotFoundException, QueryEvaluationException;
-
-   
-
-    @Override
-    public abstract void close() throws IOException;
-    
-}