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From miha...@apache.org
Subject [40/51] [partial] incubator-rya git commit: Cannot delete temp branch, doc'd it.
Date Mon, 07 Dec 2015 12:05:10 GMT
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/extras/indexing/src/main/java/mvm/rya/accumulo/mr/fileinput/RyaBatchWriterInputTool.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/accumulo/mr/fileinput/RyaBatchWriterInputTool.java b/extras/indexing/src/main/java/mvm/rya/accumulo/mr/fileinput/RyaBatchWriterInputTool.java
deleted file mode 100644
index fb80804..0000000
--- a/extras/indexing/src/main/java/mvm/rya/accumulo/mr/fileinput/RyaBatchWriterInputTool.java
+++ /dev/null
@@ -1,243 +0,0 @@
-package mvm.rya.accumulo.mr.fileinput;
-
-/*
- * 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 static com.google.common.base.Preconditions.checkNotNull;
-
-import java.io.IOException;
-import java.io.StringReader;
-
-import mvm.rya.accumulo.mr.RyaOutputFormat;
-import mvm.rya.accumulo.mr.StatementWritable;
-import mvm.rya.accumulo.mr.utils.MRUtils;
-import mvm.rya.indexing.accumulo.ConfigUtils;
-
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.conf.Configured;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.io.LongWritable;
-import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.io.Writable;
-import org.apache.hadoop.mapreduce.Job;
-import org.apache.hadoop.mapreduce.Mapper;
-import org.apache.hadoop.mapreduce.lib.input.TextInputFormat;
-import org.apache.hadoop.util.Tool;
-import org.apache.hadoop.util.ToolRunner;
-import org.apache.log4j.Logger;
-import org.openrdf.model.Resource;
-import org.openrdf.model.Statement;
-import org.openrdf.model.URI;
-import org.openrdf.model.Value;
-import org.openrdf.model.ValueFactory;
-import org.openrdf.model.impl.ValueFactoryImpl;
-import org.openrdf.rio.ParserConfig;
-import org.openrdf.rio.RDFFormat;
-import org.openrdf.rio.RDFHandlerException;
-import org.openrdf.rio.RDFParseException;
-import org.openrdf.rio.RDFParser;
-import org.openrdf.rio.Rio;
-import org.openrdf.rio.helpers.RDFHandlerBase;
-
-import com.google.common.base.Preconditions;
-
-/**
- * Take large ntrips files and use MapReduce to ingest into other indexing
- */
-public class RyaBatchWriterInputTool extends Configured implements Tool {
-    private static final Logger logger = Logger.getLogger(RyaBatchWriterInputTool.class);
-
-    @Override
-    public int run(final String[] args) throws Exception {
-        String userName = null;
-        String pwd = null;
-        String instance = null;
-        String zk = null;
-        String format = null;
-
-        final Configuration conf = getConf();
-        // conf
-        zk = conf.get(MRUtils.AC_ZK_PROP, zk);
-        instance = conf.get(MRUtils.AC_INSTANCE_PROP, instance);
-        userName = conf.get(MRUtils.AC_USERNAME_PROP, userName);
-        pwd = conf.get(MRUtils.AC_PWD_PROP, pwd);
-        format = conf.get(MRUtils.FORMAT_PROP,  RDFFormat.NTRIPLES.getName());
-
-        String auths = conf.get(MRUtils.AC_CV_PROP, "");
-
-        conf.set(MRUtils.FORMAT_PROP, format);
-        Preconditions.checkNotNull(zk, MRUtils.AC_ZK_PROP + " not set");
-        Preconditions.checkNotNull(instance, MRUtils.AC_INSTANCE_PROP + " not set");
-        Preconditions.checkNotNull(userName, MRUtils.AC_USERNAME_PROP + " not set");
-        Preconditions.checkNotNull(pwd, MRUtils.AC_PWD_PROP + " not set");
-
-        // map the config values to free text configure values
-        conf.set(ConfigUtils.CLOUDBASE_ZOOKEEPERS, zk);
-        conf.set(ConfigUtils.CLOUDBASE_INSTANCE, instance);
-        conf.set(ConfigUtils.CLOUDBASE_USER, userName);
-        conf.set(ConfigUtils.CLOUDBASE_PASSWORD, pwd);
-        conf.set(ConfigUtils.CLOUDBASE_AUTHS, auths);
-
-        final String inputDir = args[0];
-
-        String tablePrefix = conf.get(MRUtils.TABLE_PREFIX_PROPERTY, null);
-        Preconditions.checkNotNull(tablePrefix, MRUtils.TABLE_PREFIX_PROPERTY + " not set");
-
-        String docTextTable = tablePrefix + "text";
-        conf.set(ConfigUtils.FREE_TEXT_DOC_TABLENAME, docTextTable);
-
-        String docTermTable = tablePrefix + "terms";
-        conf.set(ConfigUtils.FREE_TEXT_TERM_TABLENAME, docTermTable);
-
-        String geoTable = tablePrefix + "geo";
-        conf.set(ConfigUtils.GEO_TABLENAME, geoTable);
-
-        logger.info("Loading data into tables[rya, freetext, geo]");
-        logger.info("Loading data into tables[" + docTermTable + " " + docTextTable + " " + geoTable + "]");
-
-        Job job = new Job(new Configuration(conf), "Batch Writer load data into Rya Core and Indexing Tables");
-        job.setJarByClass(this.getClass());
-
-        // setting long job
-        Configuration jobConf = job.getConfiguration();
-        jobConf.setBoolean("mapred.map.tasks.speculative.execution", false);
-
-        jobConf.setInt("mapred.task.timeout", 1000 * 60 * 60 * 24); // timeout after 1 day
-
-        job.setInputFormatClass(TextInputFormat.class);
-
-        job.setMapperClass(ParseNtripsMapper.class);
-
-        job.setNumReduceTasks(0);
-        
-        // Use Rya Output Format
-        job.setOutputFormatClass(RyaOutputFormat.class);
-        job.setOutputKeyClass(NullWritable.class);
-        job.setOutputValueClass(StatementWritable.class);
-        job.setMapOutputKeyClass(NullWritable.class);
-        job.setMapOutputValueClass(StatementWritable.class);
-
-        TextInputFormat.setInputPaths(job, new Path(inputDir));
-
-        job.waitForCompletion(true);
-
-        return 0;
-    }
-
-    public static void main(String[] args) throws Exception {
-        ToolRunner.run(new Configuration(), new RyaBatchWriterInputTool(), args);
-    }
-
-    public static class ParseNtripsMapper extends Mapper<LongWritable, Text, Writable, Statement> {
-        private static final Logger logger = Logger.getLogger(ParseNtripsMapper.class);
-
-        private RDFParser parser;
-        private RDFFormat rdfFormat;
-
-        @Override
-        protected void setup(final Context context) throws IOException, InterruptedException {
-            super.setup(context);
-            Configuration conf = context.getConfiguration();
-
-            final ValueFactory vf = new ValueFactoryImpl();
-
-            String rdfFormatName = conf.get(MRUtils.FORMAT_PROP);
-            checkNotNull(rdfFormatName, "Rdf format cannot be null");
-            rdfFormat = RDFFormat.valueOf(rdfFormatName);
-
-            String namedGraphString = conf.get(MRUtils.NAMED_GRAPH_PROP);
-            checkNotNull(namedGraphString, MRUtils.NAMED_GRAPH_PROP + " cannot be null");
-
-            final Resource namedGraph = vf.createURI(namedGraphString);
-
-            parser = Rio.createParser(rdfFormat);
-            parser.setParserConfig(new ParserConfig(true, true, true, RDFParser.DatatypeHandling.VERIFY));
-            parser.setRDFHandler(new RDFHandlerBase() {
-                @Override
-                public void handleStatement(Statement statement) throws RDFHandlerException {
-                    Statement output;
-                    if (rdfFormat.equals(RDFFormat.NTRIPLES)) {
-                        output = new ConextStatementWrapper(statement, namedGraph);
-                    } else {
-                        output = statement;
-                    }
-                    try {
-                        context.write(NullWritable.get(), new StatementWritable(output));
-                    } catch (IOException e) {
-                        logger.error("Error writing statement", e);
-                        throw new RDFHandlerException(e);
-                    } catch (InterruptedException e) {
-                        logger.error("Error writing statement", e);
-                        throw new RDFHandlerException(e);
-                    }
-                }
-
-            });
-        }
-
-        @Override
-        public void map(LongWritable key, Text value, Context output) throws IOException, InterruptedException {
-            String rdf = value.toString();
-            try {
-                parser.parse(new StringReader(rdf), "");
-            } catch (RDFParseException e) {
-                logger.error("Line[" + rdf + "] cannot be formatted with format[" + rdfFormat + "]. Exception[" + e.getMessage()
-                        + "]", e);
-            } catch (Exception e) {
-                logger.error("error during map", e);
-                throw new IOException("Exception occurred parsing triple[" + rdf + "]", e);
-            }
-        }
-    }
-
-    @SuppressWarnings("serial")
-    private static class ConextStatementWrapper implements Statement {
-        private Statement statementWithoutConext;
-        private Resource context;
-
-        public ConextStatementWrapper(Statement statementWithoutConext, Resource context) {
-            this.statementWithoutConext = statementWithoutConext;
-            this.context = context;
-        }
-
-        @Override
-        public Resource getSubject() {
-            return statementWithoutConext.getSubject();
-        }
-
-        @Override
-        public URI getPredicate() {
-            return statementWithoutConext.getPredicate();
-        }
-
-        @Override
-        public Value getObject() {
-            return statementWithoutConext.getObject();
-        }
-
-        @Override
-        public Resource getContext() {
-            return context;
-        }
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/extras/indexing/src/main/java/mvm/rya/accumulo/precompQuery/AccumuloPrecompQueryIndexer.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/accumulo/precompQuery/AccumuloPrecompQueryIndexer.java b/extras/indexing/src/main/java/mvm/rya/accumulo/precompQuery/AccumuloPrecompQueryIndexer.java
deleted file mode 100644
index 86cb73e..0000000
--- a/extras/indexing/src/main/java/mvm/rya/accumulo/precompQuery/AccumuloPrecompQueryIndexer.java
+++ /dev/null
@@ -1,326 +0,0 @@
-package mvm.rya.accumulo.precompQuery;
-
-/*
- * 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.IOException;
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.NoSuchElementException;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import org.apache.accumulo.core.client.BatchScanner;
-import org.apache.accumulo.core.client.Connector;
-import org.apache.accumulo.core.client.TableNotFoundException;
-import org.apache.accumulo.core.data.Key;
-import org.apache.accumulo.core.data.Range;
-import org.apache.accumulo.core.data.Value;
-import org.apache.accumulo.core.security.Authorizations;
-import org.apache.hadoop.io.Text;
-import org.openrdf.query.Binding;
-import org.openrdf.query.BindingSet;
-import org.openrdf.query.QueryEvaluationException;
-import org.openrdf.query.algebra.evaluation.QueryBindingSet;
-
-import com.google.common.collect.HashMultimap;
-import com.google.common.collect.Lists;
-import com.google.common.collect.Sets;
-
-import mvm.rya.indexing.PrecompQueryIndexer;
-import mvm.rya.indexing.external.tupleSet.AccumuloIndexSet.AccValueFactory;
-
-public class AccumuloPrecompQueryIndexer implements PrecompQueryIndexer {
-
-    
-    private Connector accCon;
-    private String tableName;
-    private Map<String, AccValueFactory> bindings;
-  
-    
-    
-    public AccumuloPrecompQueryIndexer(Connector accCon, String tableName) {
-        this.accCon = accCon;
-        this.tableName = tableName;
-    }
-    
-    
-    @Override
-    public void storeBindingSet(BindingSet bs) throws IOException {
-        // TODO Auto-generated method stub
-
-    }
-
-    @Override
-    public void storeBindingSets(Collection<BindingSet> bindingSets) throws IOException, IllegalArgumentException {
-        // TODO Auto-generated method stub
-
-    }
-
-    @Override
-    public CloseableIteration<BindingSet, QueryEvaluationException> queryPrecompJoin(List<String> varOrder,
-            String localityGroup, Map<String, AccValueFactory> bindings, Map<String, org.openrdf.model.Value> valMap, Collection<BindingSet> bsConstraints) 
-                    throws QueryEvaluationException, TableNotFoundException {
-        
-        
-        final int prefixLength = Integer.parseInt(varOrder.remove(varOrder.size()-1));
-        final Iterator<Entry<Key,Value>> accIter;
-        final HashMultimap<Range,BindingSet> map = HashMultimap.create();
-        final List<BindingSet> extProdList = Lists.newArrayList();
-        final Map<String, AccValueFactory> bindingMap = bindings;
-        final List<String> order = varOrder;
-        final BatchScanner bs = accCon.createBatchScanner(tableName, new Authorizations(), 10);
-        final Set<Range> ranges = Sets.newHashSet();
-        
-        
-        
-        bs.fetchColumnFamily(new Text(localityGroup));
-        
-        //process bindingSet and constant constraints
-        for (BindingSet bSet : bsConstraints) {
-            StringBuffer rangePrefix = new StringBuffer();
-            int i = 0;
-
-            for (String b : order) {
-
-                if (i >= prefixLength) {
-                    break;
-                }
-
-                if (b.startsWith("-const-")) {
-                    String val = bindings.get(b).create(valMap.get(b));
-                    rangePrefix.append(val);
-                    rangePrefix.append("\u0000");
-                } else {
-
-                    Binding v = bSet.getBinding(b);
-                    if (v == null) {
-                        throw new IllegalStateException("Binding set can't have null value!");
-                    }
-                    String val = bindings.get(b).create(bSet.getValue(b));
-                    rangePrefix.append(val);
-                    rangePrefix.append("\u0000");
-
-                }
-
-                i++;
-
-            }
-            if (rangePrefix.length() > 0) {
-                String prefixWithOutNull = rangePrefix.deleteCharAt(rangePrefix.length() - 1).toString();
-                String prefixWithNull = prefixWithOutNull + "\u0001";
-                Range r = new Range(new Key(prefixWithOutNull), true, new Key(prefixWithNull), false);
-                map.put(r, bSet);
-                ranges.add(r);
-            } else if (bSet.size() > 0) {
-                extProdList.add(bSet);
-            }
-        }
-        
-        //constant constraints and no bindingSet constraints
-        //add range of entire table if no constant constraints and
-        //bsConstraints consists of single, empty set (occurs when AIS is
-        //first node evaluated in query)
-        if (ranges.isEmpty() && bsConstraints.size() > 0) {
-
-            if (prefixLength > 0) {
-                StringBuffer rangePrefix = new StringBuffer();
-
-                int i = 0;
-                for (String b : order) {
-                    if (i >= prefixLength) {
-                        break;
-                    }
-                    if (b.startsWith("-const-")) {
-                        String val = bindings.get(b).create(valMap.get(b));
-                        rangePrefix.append(val);
-                        rangePrefix.append("\u0000");
-                    } 
-                    i++;
-                }
-
-                String prefixWithOutNull = rangePrefix.deleteCharAt(rangePrefix.length() - 1).toString();
-                String prefixWithNull = prefixWithOutNull + "\u0001";
-                Range r = new Range(new Key(prefixWithOutNull), true, new Key(prefixWithNull), false);
-                ranges.add(r);
-
-            } else { // no constant or bindingSet constraints
-                ranges.add(new Range("", true, "~", false));
-            }
-        }
-        
-        if (ranges.size() == 0) {
-            accIter = null;
-        } else {
-            bs.setRanges(ranges);
-            accIter = bs.iterator();
-        }
-
-   
-        return new CloseableIteration<BindingSet, QueryEvaluationException>() {
-
-            @Override
-            public void remove() throws QueryEvaluationException {
-                throw new UnsupportedOperationException();
-            }
-
-            private Iterator<BindingSet> inputSet = null;
-            private QueryBindingSet currentSolutionBs = null;
-            private boolean hasNextCalled = false;
-            private boolean isEmpty = false;
-           
-
-            
-            @Override
-            public BindingSet next() throws QueryEvaluationException {
-                QueryBindingSet bs = new QueryBindingSet();
-
-                if (hasNextCalled) {
-                    hasNextCalled = false;
-                    if (inputSet != null) {
-                        bs.addAll(inputSet.next());
-                    }
-                    bs.addAll(currentSolutionBs);
-                } else if (isEmpty) {
-                    throw new NoSuchElementException();
-                } else {
-                    if (this.hasNext()) {
-                        hasNextCalled = false;
-                        if (inputSet != null) {
-                            bs.addAll(inputSet.next());
-                        }
-                        bs.addAll(currentSolutionBs);
-                    } else {
-                        throw new NoSuchElementException();
-                    }
-                }
-
-                return bs;
-            }
-
-            @Override
-            public boolean hasNext() throws QueryEvaluationException {
-
-                if(accIter == null ) {
-                    isEmpty = true;
-                    return false;
-                }
-                
-                if (!hasNextCalled && !isEmpty) {
-                    while (accIter.hasNext() || (inputSet != null && inputSet.hasNext())) {
-
-                        if(inputSet != null && inputSet.hasNext()) {
-                            hasNextCalled = true;
-                            return true;
-                        }
-                        
-                        
-                        Key k = accIter.next().getKey();
-                        final String[] s = k.getRow().toString().split("\u0000");
-                       
-                        StringBuilder rangePrefix = new StringBuilder();
-                        // TODO Assuming that order specifies order of variables
-                        // commmon to
-                        // bindingSet passed in and variables in index table
-                        // --size is equal to
-                        
-                        for (int i = 0; i < prefixLength; i++) {
-                            rangePrefix.append(s[i]);
-                            rangePrefix.append("\u0000");
-                        }
-
-                        // TODO I need to remember what the type was!
-                        currentSolutionBs = new QueryBindingSet();
-                        int i = 0;
-                        for (String b : order) {
-                            if (b.startsWith("-const")) {
-                                i++;
-                            } else {
-                                final String v = s[i];
-                                currentSolutionBs.addBinding(b, bindingMap.get(b).create(v));
-                                i++;
-                            }
-
-                        }
-                        //check to see if bindingSet constraints exist
-                        if (map.size() > 0) {
-                            String prefixWithOutNull = rangePrefix.deleteCharAt(rangePrefix.length() - 1).toString();
-                            String prefixWithNull = prefixWithOutNull + "\u0001";
-                            Range r = new Range(new Key(prefixWithOutNull), true, new Key(prefixWithNull), false);
-                            inputSet = map.get(r).iterator();
-                            if (!inputSet.hasNext()) {
-                                continue;
-                            } else {
-                                hasNextCalled = true;
-                                return true;
-                            } // check to see if binding set constraints exist, but no common vars
-                        } else if (extProdList.size() > 0) {
-                            inputSet = extProdList.iterator();
-                            hasNextCalled = true;
-                            return true;
-                        }else {  //no bindingsSet constraints--only constant constraints or none
-                            hasNextCalled = true;
-                            return true;
-                        }
-                    }
-
-                    isEmpty = true;
-                    return false;
-
-                } else if (isEmpty) {
-                    return false;
-                } else {
-                    return true;
-                }
-
-            }
-
-            @Override
-            public void close() throws QueryEvaluationException {
-                bs.close();
-            }
-
-        };
-    }
-
-    
-    
-    @Override
-    public void flush() throws IOException {
-        // TODO Auto-generated method stub
-
-    }
-
-    @Override
-    public void close() throws IOException {
-        // TODO Auto-generated method stub
-
-    }
-    
-    
-    
-    
-    
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/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;
-    
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/extras/indexing/src/main/java/mvm/rya/indexing/FilterFunctionOptimizer.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/indexing/FilterFunctionOptimizer.java b/extras/indexing/src/main/java/mvm/rya/indexing/FilterFunctionOptimizer.java
deleted file mode 100644
index 5d2678b..0000000
--- a/extras/indexing/src/main/java/mvm/rya/indexing/FilterFunctionOptimizer.java
+++ /dev/null
@@ -1,358 +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 java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import mvm.rya.accumulo.AccumuloRdfConfiguration;
-import mvm.rya.indexing.IndexingFunctionRegistry.FUNCTION_TYPE;
-import mvm.rya.indexing.accumulo.ConfigUtils;
-import mvm.rya.indexing.accumulo.freetext.AccumuloFreeTextIndexer;
-import mvm.rya.indexing.accumulo.freetext.FreeTextTupleSet;
-import mvm.rya.indexing.accumulo.geo.GeoMesaGeoIndexer;
-import mvm.rya.indexing.accumulo.geo.GeoTupleSet;
-import mvm.rya.indexing.accumulo.temporal.AccumuloTemporalIndexer;
-import mvm.rya.indexing.accumulo.temporal.TemporalTupleSet;
-import mvm.rya.indexing.mongodb.MongoGeoIndexer;
-
-import org.apache.accumulo.core.client.AccumuloException;
-import org.apache.accumulo.core.client.AccumuloSecurityException;
-import org.apache.accumulo.core.client.TableExistsException;
-import org.apache.accumulo.core.client.TableNotFoundException;
-import org.apache.commons.lang.Validate;
-import org.apache.hadoop.conf.Configurable;
-import org.apache.hadoop.conf.Configuration;
-import org.geotools.feature.SchemaException;
-import org.openrdf.model.Resource;
-import org.openrdf.model.URI;
-import org.openrdf.model.Value;
-import org.openrdf.model.ValueFactory;
-import org.openrdf.model.impl.URIImpl;
-import org.openrdf.model.impl.ValueFactoryImpl;
-import org.openrdf.query.BindingSet;
-import org.openrdf.query.Dataset;
-import org.openrdf.query.algebra.And;
-import org.openrdf.query.algebra.Filter;
-import org.openrdf.query.algebra.FunctionCall;
-import org.openrdf.query.algebra.Join;
-import org.openrdf.query.algebra.LeftJoin;
-import org.openrdf.query.algebra.QueryModelNode;
-import org.openrdf.query.algebra.StatementPattern;
-import org.openrdf.query.algebra.TupleExpr;
-import org.openrdf.query.algebra.ValueConstant;
-import org.openrdf.query.algebra.ValueExpr;
-import org.openrdf.query.algebra.Var;
-import org.openrdf.query.algebra.evaluation.QueryOptimizer;
-import org.openrdf.query.algebra.helpers.QueryModelVisitorBase;
-
-import com.google.common.collect.Lists;
-
-public class FilterFunctionOptimizer implements QueryOptimizer, Configurable {
-
-    private ValueFactory valueFactory = new ValueFactoryImpl();
-    
-    private Configuration conf;
-    private GeoIndexer geoIndexer;
-    private FreeTextIndexer freeTextIndexer;
-    private TemporalIndexer temporalIndexer;
-    private boolean init = false;
-    
-    
-    public FilterFunctionOptimizer() {
-    }
-    
-    
-    public FilterFunctionOptimizer(AccumuloRdfConfiguration conf) throws AccumuloException, AccumuloSecurityException, 
-    TableNotFoundException, IOException, SchemaException, TableExistsException {
-        this.conf = conf;
-        init();
-    }
-    
-    //setConf initializes FilterFunctionOptimizer so reflection can be used
-    //to create optimizer in RdfCloudTripleStoreConnection
-    @Override
-    public void setConf(Configuration conf) {
-        this.conf = conf;
-        init();
-    }
-    
-    
-    private void init() {
-        if (!init) {
-            if (ConfigUtils.getUseMongo(conf)) {
-                this.geoIndexer = new MongoGeoIndexer();
-                geoIndexer.setConf(conf);
-            } else {
-                this.geoIndexer = new GeoMesaGeoIndexer();
-                geoIndexer.setConf(conf);
-                this.freeTextIndexer = new AccumuloFreeTextIndexer();
-                freeTextIndexer.setConf(conf);
-                this.temporalIndexer = new AccumuloTemporalIndexer();
-                temporalIndexer.setConf(conf);
-                init = true; 
-            }
-        }
-    }
-    
-    @Override
-    public void optimize(TupleExpr tupleExpr, Dataset dataset, BindingSet bindings) {
-     // find variables used in property and resource based searches:
-        SearchVarVisitor searchVars = new SearchVarVisitor();
-        tupleExpr.visit(searchVars);
-        // rewrites for property searches:
-        processPropertySearches(tupleExpr, searchVars.searchProperties);
-
-    }
-    
-    
-    
-    private void processPropertySearches(TupleExpr tupleExpr, Collection<Var> searchProperties) {
-        MatchStatementVisitor matchStatements = new MatchStatementVisitor(searchProperties);
-        tupleExpr.visit(matchStatements);
-        for (StatementPattern matchStatement: matchStatements.matchStatements) {
-            Var subject = matchStatement.getSubjectVar();
-            if (subject.hasValue() && !(subject.getValue() instanceof Resource))
-                throw new IllegalArgumentException("Query error: Found " + subject.getValue() + ", expected an URI or BNode");
-            Validate.isTrue(subject.hasValue() || subject.getName() != null);
-            Validate.isTrue(!matchStatement.getObjectVar().hasValue() && matchStatement.getObjectVar().getName() != null);
-            buildQuery(tupleExpr, matchStatement);
-        }
-        
-    }
-    
-    
-    private void buildQuery(TupleExpr tupleExpr, StatementPattern matchStatement) {
-        //If our IndexerExpr (to be) is the rhs-child of LeftJoin, we can safely make that a Join:
-        //  the IndexerExpr will (currently) not return results that can deliver unbound variables.
-        //This optimization should probably be generalized into a LeftJoin -> Join optimizer under certain conditions. Until that
-        //  has been done, this code path at least takes care of queries generated by OpenSahara SparqTool that filter on OPTIONAL
-        //  projections. E.g. summary~'full text search' (summary is optional). See #379
-        if (matchStatement.getParentNode() instanceof LeftJoin) {
-            LeftJoin leftJoin = (LeftJoin)matchStatement.getParentNode();
-            if (leftJoin.getRightArg() == matchStatement && leftJoin.getCondition() == null)
-                matchStatement.getParentNode().replaceWith(new Join(leftJoin.getLeftArg(), leftJoin.getRightArg()));
-        }
-        FilterFunction fVisitor = new FilterFunction(matchStatement.getObjectVar().getName());
-        tupleExpr.visit(fVisitor);
-        List<IndexingExpr> results = Lists.newArrayList();
-        for(int i = 0; i < fVisitor.func.size(); i++){
-            results.add(new IndexingExpr(fVisitor.func.get(i), matchStatement, fVisitor.args.get(i)));  
-        }
-        removeMatchedPattern(tupleExpr, matchStatement, new IndexerExprReplacer(results));
-        
-    }
-    
-    //find vars contained in filters
-    private static class SearchVarVisitor extends QueryModelVisitorBase<RuntimeException> {
-        
-        private final Collection<Var> searchProperties = new ArrayList<Var>(); 
-
-        @Override
-        public void meet(FunctionCall fn) {
-            URI fun = new URIImpl(fn.getURI());
-            Var result = IndexingFunctionRegistry.getResultVarFromFunctionCall(fun, fn.getArgs());
-            if (result != null && !searchProperties.contains(result))
-                searchProperties.add(result);
-        }
-    }
-
-    //find StatementPatterns containing filter variables
-    private static class MatchStatementVisitor extends QueryModelVisitorBase<RuntimeException> {
-        private final Collection<Var> propertyVars;
-        private final Collection<Var> usedVars = new ArrayList<Var>();
-        private final List<StatementPattern> matchStatements = new ArrayList<StatementPattern>();
-
-        public MatchStatementVisitor(Collection<Var> propertyVars) {
-            this.propertyVars = propertyVars;
-        }
-
-        @Override public void meet(StatementPattern statement) {
-            Var object = statement.getObjectVar();
-            if (propertyVars.contains(object))
-                if (usedVars.contains(object))
-                    throw new IllegalArgumentException("Illegal search, variable is used multiple times as object: " + object.getName());
-                else {
-                    usedVars.add(object);
-                    matchStatements.add(statement);
-                }
-        }
-    }
-
-    private abstract class AbstractEnhanceVisitor extends QueryModelVisitorBase<RuntimeException> {
-        final String matchVar;
-        List<URI> func = Lists.newArrayList();
-        List<Value[]> args = Lists.newArrayList();
-
-        public AbstractEnhanceVisitor(String matchVar) {
-            this.matchVar = matchVar;
-        }
-
-        protected void addFilter(URI uri, Value[] values) {
-            func.add(uri);
-            args.add(values);
-        }
-    }
-
-    //create indexing expression for each filter matching var in filter StatementPattern
-    //replace old filter condition with true condition
-    private class FilterFunction extends AbstractEnhanceVisitor {
-        public FilterFunction(String matchVar) {
-            super(matchVar);
-        }
-
-        @Override
-        public void meet(FunctionCall call) {
-            URI fnUri = valueFactory.createURI(call.getURI());
-            Var resultVar = IndexingFunctionRegistry.getResultVarFromFunctionCall(fnUri, call.getArgs());
-            if (resultVar != null && resultVar.getName().equals(matchVar)) {
-                addFilter(valueFactory.createURI(call.getURI()), extractArguments(matchVar, call));
-                if (call.getParentNode() instanceof Filter || call.getParentNode() instanceof And || call.getParentNode() instanceof LeftJoin)
-                    call.replaceWith(new ValueConstant(valueFactory.createLiteral(true)));
-                else
-                    throw new IllegalArgumentException("Query error: Found " + call + " as part of an expression that is too complex");
-            }
-        }
-
-
-        private Value[] extractArguments(String matchName, FunctionCall call) {
-            Value args[] = new Value[call.getArgs().size() - 1];
-            int argI = 0;
-            for (int i = 0; i != call.getArgs().size(); ++i) {
-                ValueExpr arg = call.getArgs().get(i);
-                if (argI == i && arg instanceof Var && matchName.equals(((Var)arg).getName()))
-                    continue;
-                if (arg instanceof ValueConstant)
-                    args[argI] = ((ValueConstant)arg).getValue();
-                else if (arg instanceof Var && ((Var)arg).hasValue())
-                    args[argI] = ((Var)arg).getValue();
-                else
-                    throw new IllegalArgumentException("Query error: Found " + arg + ", expected a Literal, BNode or URI");
-                ++argI;
-            }
-            return args;
-        }
-
-        @Override
-        public void meet(Filter filter) {
-            //First visit children, then condition (reverse of default):
-            filter.getArg().visit(this);
-            filter.getCondition().visit(this);
-        }
-    }
-
-    private void removeMatchedPattern(TupleExpr tupleExpr, StatementPattern pattern, TupleExprReplacer replacer) {
-        List<TupleExpr> indexTuples = replacer.createReplacement(pattern);
-        if (indexTuples.size() > 1) {
-            VarExchangeVisitor vev = new VarExchangeVisitor(pattern);
-            tupleExpr.visit(vev);
-            Join join = new Join(indexTuples.remove(0), indexTuples.remove(0));
-            for (TupleExpr geo : indexTuples) {
-                join = new Join(join, geo);
-            }
-            pattern.replaceWith(join);
-        } else if (indexTuples.size() == 1) {
-            pattern.replaceWith(indexTuples.get(0));
-            pattern.setParentNode(null);
-        } else {
-            throw new IllegalStateException("Must have at least one replacement for matched StatementPattern.");
-        }
-    }
-
-    private interface TupleExprReplacer {
-        List<TupleExpr> createReplacement(TupleExpr org);
-    }
-
-    
-    //replace each filter pertinent StatementPattern with corresponding index expr
-    private class IndexerExprReplacer implements TupleExprReplacer {
-        private final List<IndexingExpr> indxExpr;
-        private FUNCTION_TYPE type;
-
-        public IndexerExprReplacer(List<IndexingExpr> indxExpr) {
-            this.indxExpr = indxExpr;
-            URI func = indxExpr.get(0).getFunction();
-            this.type = IndexingFunctionRegistry.getFunctionType(func);
-        }
-
-        @Override
-        public List<TupleExpr> createReplacement(TupleExpr org) {
-            List<TupleExpr> indexTuples = Lists.newArrayList();
-            switch (type) {
-            case GEO:
-                for (IndexingExpr indx : indxExpr) {
-                    indexTuples.add(new GeoTupleSet(indx, geoIndexer));
-                }
-                break;
-            case FREETEXT:
-                for (IndexingExpr indx : indxExpr) {
-                    indexTuples.add(new FreeTextTupleSet(indx, freeTextIndexer));
-                }
-                break;
-            case TEMPORAL:
-                for (IndexingExpr indx : indxExpr) {
-                    indexTuples.add(new TemporalTupleSet(indx, temporalIndexer));
-                }
-                break;
-            default:
-                throw new IllegalArgumentException("Incorrect type!");
-
-            }
-            return indexTuples;
-        }
-    }
-    
-    
-    private static class VarExchangeVisitor extends QueryModelVisitorBase<RuntimeException> {
-
-        private final  StatementPattern exchangeVar;
-              
-        public VarExchangeVisitor(StatementPattern sp) {
-            this.exchangeVar = sp;
-        }
-
-        @Override
-        public void meet(Join node) {
-            QueryModelNode lNode = node.getLeftArg();
-            if (lNode instanceof StatementPattern) {
-                exchangeVar.replaceWith(lNode);
-                node.setLeftArg(exchangeVar);
-            } else {
-                super.meet(node);
-            }
-        }
-    }
-    
-    
-   
-
-
-
-    @Override
-    public Configuration getConf() {
-        return conf;
-    }
-    
-    
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/extras/indexing/src/main/java/mvm/rya/indexing/FreeTextIndexer.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/indexing/FreeTextIndexer.java b/extras/indexing/src/main/java/mvm/rya/indexing/FreeTextIndexer.java
deleted file mode 100644
index 2d8bae9..0000000
--- a/extras/indexing/src/main/java/mvm/rya/indexing/FreeTextIndexer.java
+++ /dev/null
@@ -1,62 +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.IOException;
-import java.util.Set;
-
-import mvm.rya.api.persist.index.RyaSecondaryIndexer;
-
-import org.openrdf.model.Statement;
-import org.openrdf.model.URI;
-import org.openrdf.query.QueryEvaluationException;
-
-/**
- * A repository to store, index, and retrieve {@link Statement}s based on freetext features.
- */
-public interface FreeTextIndexer extends RyaSecondaryIndexer {
-
-	/**
-	 * Query the Free Text Index with specific constraints. A <code>null</code> or empty parameters imply no constraint.
-	 * 
-	 * @param query
-	 *            the query to perform
-	 * @param contraints
-	 *            the constraints on the statements returned
-	 * @return the set of statements that meet the query and other constraints.
-	 * @throws IOException
-	 */
-	public abstract CloseableIteration<Statement, QueryEvaluationException> queryText(String query, StatementContraints contraints) throws IOException;
-
-	/**
-	 * @return the set of predicates indexed by the indexer.
-	 */
-	public abstract Set<URI> getIndexablePredicates();
-
-	@Override
-	public abstract void flush() throws IOException;
-
-	@Override
-	public abstract void close() throws IOException;
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/extras/indexing/src/main/java/mvm/rya/indexing/GeoIndexer.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/indexing/GeoIndexer.java b/extras/indexing/src/main/java/mvm/rya/indexing/GeoIndexer.java
deleted file mode 100644
index 7c04903..0000000
--- a/extras/indexing/src/main/java/mvm/rya/indexing/GeoIndexer.java
+++ /dev/null
@@ -1,201 +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.IOException;
-import java.util.Set;
-
-import mvm.rya.api.persist.index.RyaSecondaryIndexer;
-
-import org.openrdf.model.Statement;
-import org.openrdf.model.URI;
-import org.openrdf.query.QueryEvaluationException;
-
-import com.vividsolutions.jts.geom.Geometry;
-
-/**
- * A repository to store, index, and retrieve {@link Statement}s based on geospatial features.
- */
-public interface GeoIndexer extends RyaSecondaryIndexer {
-	/**
-	 * Returns statements that contain a geometry that is equal to the queried {@link Geometry} and meet the {@link StatementContraints}.
-	 * 
-	 * <p>
-	 * From Wikipedia (http://en.wikipedia.org/wiki/DE-9IM):
-	 * <ul>
-	 * <li>
-	 * "Two geometries are topologically equal if their interiors intersect and no part of the interior or boundary of one geometry intersects the exterior of the other"
-	 * <li>"A is equal to B if A is within B and A contains B"
-	 * </ul>
-	 * 
-	 * @param query
-	 *            the queried geometry
-	 * @param contraints
-	 *            the {@link StatementContraints}
-	 * @return
-	 */
-	public abstract CloseableIteration<Statement, QueryEvaluationException> queryEquals(Geometry query, StatementContraints contraints);
-
-	/**
-	 * Returns statements that contain a geometry that is disjoint to the queried {@link Geometry} and meet the {@link StatementContraints}.
-	 * 
-	 * <p>
-	 * From Wikipedia (http://en.wikipedia.org/wiki/DE-9IM):
-	 * <ul>
-	 * <li>"A and B are disjoint if they have no point in common. They form a set of disconnected geometries."
-	 * <li>"A and B are disjoint if A does not intersect B"
-	 * </ul>
-	 * 
-	 * @param query
-	 *            the queried geometry
-	 * @param contraints
-	 *            the {@link StatementContraints}
-	 * @return
-	 */
-	public abstract CloseableIteration<Statement, QueryEvaluationException> queryDisjoint(Geometry query, StatementContraints contraints);
-
-	/**
-	 * Returns statements that contain a geometry that Intersects the queried {@link Geometry} and meet the {@link StatementContraints}.
-	 * 
-	 * <p>
-	 * From Wikipedia (http://en.wikipedia.org/wiki/DE-9IM):
-	 * <ul>
-	 * <li>"a intersects b: geometries a and b have at least one point in common."
-	 * <li>"not Disjoint"
-	 * </ul>
-	 * 
-	 * 
-	 * @param query
-	 *            the queried geometry
-	 * @param contraints
-	 *            the {@link StatementContraints}
-	 * @return
-	 */
-	public abstract CloseableIteration<Statement, QueryEvaluationException> queryIntersects(Geometry query, StatementContraints contraints);
-
-	/**
-	 * Returns statements that contain a geometry that Touches the queried {@link Geometry} and meet the {@link StatementContraints}.
-	 * 
-	 * <p>
-	 * From Wikipedia (http://en.wikipedia.org/wiki/DE-9IM):
-	 * <ul>
-	 * <li>"a touches b, they have at least one boundary point in common, but no interior points."
-	 * </ul>
-	 * 
-	 * 
-	 * @param query
-	 *            the queried geometry
-	 * @param contraints
-	 *            the {@link StatementContraints}
-	 * @return
-	 */
-	public abstract CloseableIteration<Statement, QueryEvaluationException> queryTouches(Geometry query, StatementContraints contraints);
-
-	/**
-	 * Returns statements that contain a geometry that crosses the queried {@link Geometry} and meet the {@link StatementContraints}.
-	 * 
-	 * <p>
-	 * From Wikipedia (http://en.wikipedia.org/wiki/DE-9IM):
-	 * <ul>
-	 * <li>
-	 * "a crosses b, they have some but not all interior points in common (and the dimension of the intersection is less than that of at least one of them)."
-	 * </ul>
-	 * 
-	 * @param query
-	 *            the queried geometry
-	 * @param contraints
-	 *            the {@link StatementContraints}
-	 * @return
-	 */
-	public abstract CloseableIteration<Statement, QueryEvaluationException> queryCrosses(Geometry query, StatementContraints contraints);
-
-	/**
-	 * Returns statements that contain a geometry that is Within the queried {@link Geometry} and meet the {@link StatementContraints}.
-	 * 
-	 * <p>
-	 * From Wikipedia (http://en.wikipedia.org/wiki/DE-9IM):
-	 * <ul>
-	 * <li>"a is within b, a lies in the interior of b"
-	 * <li>Same as: "Contains(b,a)"
-	 * </ul>
-	 * 
-	 * 
-	 * @param query
-	 *            the queried geometry
-	 * @param contraints
-	 *            the {@link StatementContraints}
-	 * @return
-	 */
-	public abstract CloseableIteration<Statement, QueryEvaluationException> queryWithin(Geometry query, StatementContraints contraints);
-
-	/**
-	 * Returns statements that contain a geometry that Contains the queried {@link Geometry} and meet the {@link StatementContraints}.
-	 * 
-	 * <p>
-	 * From Wikipedia (http://en.wikipedia.org/wiki/DE-9IM):
-	 * <ul>
-	 * <li>b is within a. Geometry b lies in the interior of a. Another definition:
-	 * "a 'contains' b iff no points of b lie in the exterior of a, and at least one point of the interior of b lies in the interior of a"
-	 * <li>Same: Within(b,a)
-	 * </ul>
-	 * 
-	 * 
-	 * @param query
-	 *            the queried geometry
-	 * @param contraints
-	 *            the {@link StatementContraints}
-	 * @return
-	 */
-	public abstract CloseableIteration<Statement, QueryEvaluationException> queryContains(Geometry query, StatementContraints contraints);
-
-	/**
-	 * Returns statements that contain a geometry that Overlaps the queried {@link Geometry} and meet the {@link StatementContraints}.
-	 * 
-	 * <p>
-	 * From Wikipedia (http://en.wikipedia.org/wiki/DE-9IM):
-	 * <ul>
-	 * <li>a crosses b, they have some but not all interior points in common (and the dimension of the intersection is less than that of at
-	 * least one of them).
-	 * </ul>
-	 * 
-	 * 
-	 * @param query
-	 *            the queried geometry
-	 * @param contraints
-	 *            the {@link StatementContraints}
-	 * @return
-	 */
-	public abstract CloseableIteration<Statement, QueryEvaluationException> queryOverlaps(Geometry query, StatementContraints contraints);
-
-	/**
-	 * @return the set of predicates indexed by the indexer.
-	 */
-	public abstract Set<URI> getIndexablePredicates();
-
-	@Override
-	public abstract void flush() throws IOException;
-
-	@Override
-	public abstract void close() throws IOException;
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/ExternalIndexMatcher.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/ExternalIndexMatcher.java b/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/ExternalIndexMatcher.java
deleted file mode 100644
index ee3d444..0000000
--- a/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/ExternalIndexMatcher.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package mvm.rya.indexing.IndexPlanValidator;
-
-/*
- * 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 java.util.Iterator;
-
-import org.openrdf.query.algebra.TupleExpr;
-
-public interface ExternalIndexMatcher {
-    
-    
-    public Iterator<TupleExpr> getIndexedTuples();
-   
-    
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/GeneralizedExternalProcessor.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/GeneralizedExternalProcessor.java b/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/GeneralizedExternalProcessor.java
deleted file mode 100644
index 27a0d15..0000000
--- a/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/GeneralizedExternalProcessor.java
+++ /dev/null
@@ -1,730 +0,0 @@
-package mvm.rya.indexing.IndexPlanValidator;
-
-/*
- * 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 java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import mvm.rya.indexing.external.QueryVariableNormalizer.VarCollector;
-import mvm.rya.indexing.external.tupleSet.ExternalTupleSet;
-
-import org.openrdf.query.algebra.BindingSetAssignment;
-import org.openrdf.query.algebra.Filter;
-import org.openrdf.query.algebra.Join;
-import org.openrdf.query.algebra.Projection;
-import org.openrdf.query.algebra.QueryModelNode;
-import org.openrdf.query.algebra.StatementPattern;
-import org.openrdf.query.algebra.TupleExpr;
-import org.openrdf.query.algebra.Var;
-import org.openrdf.query.algebra.helpers.QueryModelVisitorBase;
-import org.openrdf.query.algebra.helpers.StatementPatternCollector;
-
-import com.google.common.collect.Lists;
-import com.google.common.collect.Sets;
-
-/**
- * Processes a {@link TupleExpr} and replaces sets of elements in the tree with {@link ExternalTupleSet} objects.
- */
-public class GeneralizedExternalProcessor {
-
-
-    /**
-     * Iterates through list of normalized indexes and replaces all subtrees of query which match index with index.
-     * 
-     * @param query
-     * @return TupleExpr
-     */
-    public static TupleExpr process(TupleExpr query, List<ExternalTupleSet> indexSet) {
-        
-        boolean indexPlaced = false;
-        TupleExpr rtn = query.clone();
-                
-        
-        //TODO optimization: turn on when testing done
-        QueryNodeCount qnc = new QueryNodeCount();
-        rtn.visit(qnc);
-        
-        if(qnc.getNodeCount()/2 < indexSet.size()) {
-            return null;
-        }
-
-        
-        //move BindingSetAssignment Nodes out of the way
-        organizeBSAs(rtn);
-        
-        
-        // test to see if query contains no other nodes
-        // than filter, join, projection, and statement pattern and
-        // test whether query contains duplicate StatementPatterns and filters
-        if (isTupleValid(rtn)) {
-
-            for (ExternalTupleSet index : indexSet) {
-
-                // test to see if index contains at least one StatementPattern,
-                // that StatementPatterns are unique,
-                // and that all variables found in filters occur in some
-                // StatementPattern
-                if (isTupleValid(index.getTupleExpr())) {
-
-                    ExternalTupleSet eTup = (ExternalTupleSet) index.clone();
-                    SPBubbleDownVisitor indexVistor = new SPBubbleDownVisitor(eTup);
-                    rtn.visit(indexVistor);
-                    FilterBubbleManager fbmv = new FilterBubbleManager(eTup);
-                    rtn.visit(fbmv);
-                    SubsetEqualsVisitor subIndexVis = new SubsetEqualsVisitor(eTup, rtn);
-                    rtn.visit(subIndexVis);
-                    indexPlaced = subIndexVis.indexPlaced();
-                    if(!indexPlaced) {
-                        break;
-                    }
-
-                }
-
-            }
-            if(indexPlaced) {
-//                if(indexSet.size() == 3) {
-//                    System.out.println("IndexSet is " + indexSet);
-//                    System.out.println("Tuple is " + rtn);
-//                }
-                return rtn;
-            } else {
-//                if(indexSet.size() == 3) {
-//                    System.out.println("IndexSet is " + indexSet);
-//                }
-//               
-                return null;
-            }
-            
-        } else {
-            throw new IllegalArgumentException("Invalid Query.");
-        }
-    }
-    
-    
-    
-
-
-    // determines whether query is valid, which requires that a
-    // query must contain a StatementPattern, not contain duplicate
-    // Statement Patterns or Filters, not be comprised of only Projection,
-    // Join, StatementPattern, and Filter nodes, and that any variable
-    // appearing in a Filter must appear in a StatementPattern.
-    private static boolean isTupleValid(QueryModelNode node) {
-
-        ValidQueryVisitor vqv = new ValidQueryVisitor();
-        node.visit(vqv);
-
-        Set<String> spVars = getVarNames(getQNodes("sp", node));
-
-        if (vqv.isValid() && (spVars.size() > 0)) {
-
-            FilterCollector fvis = new FilterCollector();
-            node.visit(fvis);
-            List<QueryModelNode> fList = fvis.getFilters();
-            return (fList.size() == Sets.newHashSet(fList).size() && getVarNames(fList).size() <= spVars.size());
-
-        } else {
-            return false;
-        }
-    }
-
-    private static Set<QueryModelNode> getQNodes(QueryModelNode queryNode) {
-        Set<QueryModelNode> rtns = new HashSet<QueryModelNode>();
-
-        StatementPatternCollector spc = new StatementPatternCollector();
-        queryNode.visit(spc);
-        rtns.addAll(spc.getStatementPatterns());
-
-        FilterCollector fvis = new FilterCollector();
-        queryNode.visit(fvis);
-        rtns.addAll(fvis.getFilters());
-
-        ExternalTupleCollector eVis = new ExternalTupleCollector();
-        queryNode.visit(eVis);
-        rtns.addAll(eVis.getExtTup());
-
-        return rtns;
-    }
-
-    private static Set<QueryModelNode> getQNodes(String node, QueryModelNode queryNode) {
-
-        if (node.equals("sp")) {
-            Set<QueryModelNode> eSet = new HashSet<QueryModelNode>();
-            StatementPatternCollector spc = new StatementPatternCollector();
-            queryNode.visit(spc);
-            List<StatementPattern> spList = spc.getStatementPatterns();
-            eSet.addAll(spList);
-            // returns empty set if list contains duplicate StatementPatterns
-            if (spList.size() > eSet.size()) {
-                return Sets.newHashSet();
-            } else {
-                return eSet;
-            }
-        } else if (node.equals("filter")) {
-
-            FilterCollector fvis = new FilterCollector();
-            queryNode.visit(fvis);
-
-            return Sets.newHashSet(fvis.getFilters());
-        } else {
-
-            throw new IllegalArgumentException("Invalid node type.");
-        }
-    }
-
-    // moves StatementPatterns in query that also occur in index to bottom of
-    // query tree.
-    private static class SPBubbleDownVisitor extends QueryModelVisitorBase<RuntimeException> {
-
-        private TupleExpr tuple;
-        private QueryModelNode indexQNode;
-        private Set<QueryModelNode> sSet = Sets.newHashSet();
-
-        public SPBubbleDownVisitor(ExternalTupleSet index) {
-
-            this.tuple = index.getTupleExpr();
-            indexQNode = ((Projection) tuple).getArg();
-            sSet = getQNodes("sp", indexQNode);
-
-        }
-
-        public void meet(Projection node) {
-            // moves external tuples above statement patterns before attempting
-            // to bubble down index statement patterns found in query tree
-            
-            organizeExtTuples(node);
-            
-            super.meet(node);
-        }
-
-        public void meet(Join node) {
-            // if right node contained in index, move it to bottom of query tree
-            if (sSet.contains(node.getRightArg())) {
-
-                Set<QueryModelNode> eSet = getQNodes("sp", node);
-                Set<QueryModelNode> compSet = Sets.difference(eSet, sSet);
-
-                if (eSet.containsAll(sSet)) {
-
-                    QNodeExchanger qne = new QNodeExchanger(node.getRightArg(), compSet);
-                    node.visit(qne);
-                    node.replaceChildNode(node.getRightArg(), qne.getReplaced());
-
-                    super.meet(node);
-                }
-                return;
-            }
-            // if left node contained in index, move it to bottom of query tree
-            else if (sSet.contains(node.getLeftArg())) {
-
-                Set<QueryModelNode> eSet = getQNodes("sp", node);
-                Set<QueryModelNode> compSet = Sets.difference(eSet, sSet);
-
-                if (eSet.containsAll(sSet)) {
-
-                    QNodeExchanger qne = new QNodeExchanger(node.getLeftArg(), compSet);
-                    node.visit(qne);
-                    node.replaceChildNode(node.getLeftArg(), qne.getReplaced());
-
-                    super.meet(node);
-                }
-                return;
-
-            } else {
-                super.meet(node);
-            }
-
-        }
-
-        // moves all ExternalTupleSets in query tree above remaining
-        // StatementPatterns
-        private static void organizeExtTuples(QueryModelNode node) {
-
-            ExternalTupleCollector eVis = new ExternalTupleCollector();
-            node.visit(eVis);
-
-            ExtTupleExchangeVisitor oev = new ExtTupleExchangeVisitor(eVis.getExtTup());
-            node.visit(oev);
-        }
-
-    }
-
-    // given a replacement QueryModelNode and compSet, this visitor replaces the
-    // first
-    // element in the query tree that occurs in compSet with replacement and
-    // returns
-    // the element that was replaced.
-    private static class QNodeExchanger extends QueryModelVisitorBase<RuntimeException> {
-
-        private QueryModelNode toBeReplaced;
-        private QueryModelNode replacement;
-        private Set<QueryModelNode> compSet;
-
-        public QNodeExchanger(QueryModelNode replacement, Set<QueryModelNode> compSet) {
-            this.replacement = replacement;
-            this.toBeReplaced = replacement;
-            this.compSet = compSet;
-        }
-
-        public QueryModelNode getReplaced() {
-            return toBeReplaced;
-        }
-
-        public void meet(Join node) {
-
-            if (compSet.contains(node.getRightArg())) {
-                this.toBeReplaced = node.getRightArg();
-                node.replaceChildNode(node.getRightArg(), replacement);
-                return;
-            } else if (compSet.contains(node.getLeftArg())) {
-                this.toBeReplaced = node.getLeftArg();
-                node.replaceChildNode(node.getLeftArg(), replacement);
-                return;
-            } else {
-                super.meet(node);
-            }
-
-        }
-
-    }
-
-    // moves filter that occurs in both query and index down the query tree so
-    // that that it is positioned
-    // above statement patterns associated with index. Precondition for calling
-    // this method is that
-    // SPBubbleDownVisitor has been called to position index StatementPatterns
-    // within query tree.
-    //TODO this visitor assumes that all filters are positioned at top of query tree
-    //could lead to problems if filter optimizer called before external processor
-    private static class FilterBubbleDownVisitor extends QueryModelVisitorBase<RuntimeException> {
-
-        private QueryModelNode filter;
-        private Set<QueryModelNode> compSet;
-        private boolean filterPlaced = false;
-
-        public FilterBubbleDownVisitor(QueryModelNode filter, Set<QueryModelNode> compSet) {
-            this.filter = filter;
-            this.compSet = compSet;
-
-        }
-
-        public boolean filterPlaced() {
-            return filterPlaced;
-        }
-
-        public void meet(Join node) {
-
-            if (!compSet.contains(node.getRightArg())) {
-                // looks for placed to position filter node. if right node is
-                // contained in index
-                // and left node is statement pattern node contained in index or
-                // is a join, place
-                // filter above join.
-                if (node.getLeftArg() instanceof Join || !(compSet.contains(node.getLeftArg()))) {
-                    
-                    QueryModelNode pNode = node.getParentNode();
-                    ((Filter) filter).setArg(node);
-                    pNode.replaceChildNode(node, filter);
-                    filterPlaced = true;
-                    
-                    return;
-                } // otherwise place filter below join and above right arg
-                else {
-                    ((Filter) filter).setArg(node.getRightArg());
-                    node.replaceChildNode(node.getRightArg(), filter);
-                    filterPlaced = true;
-                    return;
-
-                }
-            } else if ((node.getLeftArg() instanceof StatementPattern) && !compSet.contains(node.getLeftArg())) {
-                
-                ((Filter) filter).setArg(node.getLeftArg());
-                node.replaceChildNode(node.getLeftArg(), filter);
-                filterPlaced = true;
-                
-                return;
-            } else {
-                super.meet(node);
-            }
-        }
-
-    }
-
-    private static Set<String> getVarNames(Collection<QueryModelNode> nodes) {
-
-        List<String> tempVars;
-        Set<String> nodeVarNames = Sets.newHashSet();
-
-        for (QueryModelNode s : nodes) {
-            tempVars = VarCollector.process(s);
-            for (String t : tempVars)
-                nodeVarNames.add(t);
-        }
-        return nodeVarNames;
-
-    }
-
-    // visitor which determines whether or not to reposition a filter by calling
-    // FilterBubbleDownVisitor
-    private static class FilterBubbleManager extends QueryModelVisitorBase<RuntimeException> {
-
-        private TupleExpr tuple;
-        private QueryModelNode indexQNode;
-        private Set<QueryModelNode> sSet = Sets.newHashSet();
-        private Set<QueryModelNode> bubbledFilters = Sets.newHashSet();
-
-        public FilterBubbleManager(ExternalTupleSet index) {
-            this.tuple = index.getTupleExpr();
-            indexQNode = ((Projection) tuple).getArg();
-            sSet = getQNodes(indexQNode);
-
-        }
-
-        public void meet(Filter node) {
-
-            Set<QueryModelNode> eSet = getQNodes(node);
-            Set<QueryModelNode> compSet = Sets.difference(eSet, sSet);
-
-            // if index contains filter node and it hasn't already been moved,
-            // move it down
-            // query tree just above position of statement pattern nodes found
-            // in both query tree
-            // and index (assuming that SPBubbleDownVisitor has already been
-            // called)
-            if (sSet.contains(node.getCondition()) && !bubbledFilters.contains(node.getCondition())) {
-                FilterBubbleDownVisitor fbdv = new FilterBubbleDownVisitor((Filter) node.clone(), compSet);
-                node.visit(fbdv);
-                bubbledFilters.add(node.getCondition());
-                // checks if filter correctly placed, and if it has been,
-                // removes old copy of filter
-                if (fbdv.filterPlaced()) {
-
-                    QueryModelNode pNode = node.getParentNode();
-                    TupleExpr cNode = node.getArg();
-                    pNode.replaceChildNode(node, cNode);
-                   
-
-                    super.meetNode(pNode);
-                }
-                super.meet(node);
-
-            } else {
-                super.meet(node);
-            }
-        }
-    }
-
-    // iterates through the query tree and attempts to match subtrees with
-    // index. When a match is
-    // found, the subtree is replaced by an ExternalTupleSet formed from the
-    // index. Pre-condition for
-    // calling this method is that both SPBubbleDownVisitor and
-    // FilterBubbleManager have been called
-    // to position the StatementPatterns and Filters.
-    private static class SubsetEqualsVisitor extends QueryModelVisitorBase<RuntimeException> {
-
-        private TupleExpr query;
-        private TupleExpr tuple;
-        private QueryModelNode indexQNode;
-        private ExternalTupleSet set;
-        private Set<QueryModelNode> sSet = Sets.newHashSet();
-        private TupleExpr temp;
-        private boolean indexPlaced = false;
-        
-
-        public SubsetEqualsVisitor(ExternalTupleSet index, TupleExpr query) {
-            this.query = query;
-            this.tuple = index.getTupleExpr();
-            this.set = index;
-            indexQNode = ((Projection) tuple).getArg();
-            sSet = getQNodes(indexQNode);
-
-        }
-        
-        public boolean indexPlaced() {
-            return indexPlaced;
-        }
-        
-
-        public void meet(Join node) {
-
-            Set<QueryModelNode> eSet = getQNodes(node);
-
-            if (eSet.containsAll(sSet) && !(node.getRightArg() instanceof BindingSetAssignment)) {
-
-//                System.out.println("Eset is " + eSet + " and sSet is " + sSet);
-                
-                if (eSet.equals(sSet)) {
-                    node.replaceWith(set);
-                    indexPlaced = true;
-                    return;
-                } else {
-                    if (node.getLeftArg() instanceof StatementPattern && sSet.size() == 1) {
-                        if(sSet.contains(node.getLeftArg())) {
-                            node.setLeftArg(set);
-                            indexPlaced = true;
-                        } else if(sSet.contains(node.getRightArg())) {
-                            node.setRightArg(set);
-                            indexPlaced = true;
-                        } else {
-                            return;
-                        }
-                    }
-                    else {
-                        super.meet(node);
-                    }
-                }
-            } else if (eSet.containsAll(sSet)) {
-
-                super.meet(node);
-
-            } else {
-                return;
-            }
-
-        }
-      //TODO might need to include BindingSetAssignment Condition here
-      //to account for index consisting of only filter and BindingSetAssignment nodes
-        public void meet(Filter node) {
-
-            Set<QueryModelNode> eSet = getQNodes(node);
-
-            if (eSet.containsAll(sSet)) {
-
-                if (eSet.equals(sSet)) {
-                    node.replaceWith(set);
-                    indexPlaced = true;
-                    return;
-                } else {
-                    node.getArg().visit(this);
-                }
-            }
-        }
-        
-        
-        public void meet(StatementPattern node) {
-            return;
-        }
-    }
-
-    // visitor which determines whether a query is valid (i.e. it does not
-    // contain nodes other than
-    // Projection, Join, Filter, StatementPattern )
-    private static class ValidQueryVisitor extends QueryModelVisitorBase<RuntimeException> {
-
-        private boolean isValid = true;
-
-        public boolean isValid() {
-            return isValid;
-        }
-
-        public void meet(Projection node) {
-            node.getArg().visit(this);
-        }
-
-        public void meet(Filter node) {
-            node.getArg().visit(this);
-        }
-        
-      
-       
-        
-       
-        public void meetNode(QueryModelNode node) {
-
-            if (!((node instanceof Join) || (node instanceof StatementPattern) || (node instanceof BindingSetAssignment) || (node instanceof Var))) {
-                isValid = false;
-                return;
-           
-            } else{
-                super.meetNode(node);
-            }
-        }
-
-    }
-
-    // repositions ExternalTuples above StatementPatterns within query tree
-    private static class ExtTupleExchangeVisitor extends QueryModelVisitorBase<RuntimeException> {
-
-        private Set<QueryModelNode> extTuples;
-
-        public ExtTupleExchangeVisitor(Set<QueryModelNode> extTuples) {
-            this.extTuples = extTuples;
-        }
-
-        public void meet(Join queryNode) {
-
-            // if query tree contains external tuples and they are not
-            // positioned above statement pattern node
-            // reposition
-            if (this.extTuples.size() > 0 && !(queryNode.getRightArg() instanceof ExternalTupleSet)
-                    && !(queryNode.getRightArg() instanceof BindingSetAssignment)) {
-                
-                if (queryNode.getLeftArg() instanceof ExternalTupleSet) {
-                    QueryModelNode temp = queryNode.getLeftArg();
-                    queryNode.setLeftArg(queryNode.getRightArg());
-                    queryNode.setRightArg((TupleExpr)temp);
-                } else {
-
-                    QNodeExchanger qnev = new QNodeExchanger((QueryModelNode) queryNode.getRightArg(), this.extTuples);
-                    queryNode.visit(qnev);
-                    queryNode.replaceChildNode(queryNode.getRightArg(), qnev.getReplaced());
-                    super.meet(queryNode);
-                }
-            } else {
-                super.meet(queryNode);
-            }
-
-        }
-
-    }
-
-    private static class ExternalTupleCollector extends QueryModelVisitorBase<RuntimeException> {
-
-        private Set<QueryModelNode> eSet = new HashSet<QueryModelNode>();
-
-        @Override
-        public void meetNode(QueryModelNode node) throws RuntimeException {
-            if (node instanceof ExternalTupleSet) {
-                eSet.add(node);
-            }
-            super.meetNode(node);
-        }
-
-        public Set<QueryModelNode> getExtTup() {
-            return eSet;
-        }
-
-    }
-
-    private static class FilterCollector extends QueryModelVisitorBase<RuntimeException> {
-
-        private List<QueryModelNode> filterList = Lists.newArrayList();
-
-        public List<QueryModelNode> getFilters() {
-            return filterList;
-        }
-
-        @Override
-        public void meet(Filter node) {
-            filterList.add(node.getCondition());
-            super.meet(node);
-        }
-
-    }
-
-    private static void organizeBSAs(QueryModelNode node) {
-
-        BindingSetAssignmentCollector bsac = new BindingSetAssignmentCollector();
-        node.visit(bsac);
-
-        if (bsac.containsBSAs()) {
-            Set<QueryModelNode> bsaSet = bsac.getBindingSetAssignments();
-            BindingSetAssignmentExchangeVisitor bsaev = new BindingSetAssignmentExchangeVisitor(bsaSet);
-            node.visit(bsaev);
-        }
-    }
-
-    // repositions ExternalTuples above StatementPatterns within query tree
-    private static class BindingSetAssignmentExchangeVisitor extends QueryModelVisitorBase<RuntimeException> {
-
-        private Set<QueryModelNode> bsas;
-
-        public BindingSetAssignmentExchangeVisitor(Set<QueryModelNode> bsas) {
-            this.bsas = bsas;
-        }
-
-        public void meet(Join queryNode) {
-
-            // if query tree contains external tuples and they are not
-            // positioned above statement pattern node
-            // reposition
-            if (this.bsas.size() > 0 && !(queryNode.getRightArg() instanceof BindingSetAssignment)) {
-                QNodeExchanger qnev = new QNodeExchanger((QueryModelNode) queryNode.getRightArg(), bsas);
-                queryNode.visit(qnev);
-                queryNode.replaceChildNode(queryNode.getRightArg(), qnev.getReplaced());
-                super.meet(queryNode);
-            } else {
-                super.meet(queryNode);
-            }
-
-        }
-
-    }
-        
-        
-    public static class BindingSetAssignmentCollector extends QueryModelVisitorBase<RuntimeException> {
-
-        private Set<QueryModelNode> bindingSetList = Sets.newHashSet();
-
-        public Set<QueryModelNode> getBindingSetAssignments() {
-            return bindingSetList;
-        }
-
-        public boolean containsBSAs() {
-            return (bindingSetList.size() > 0);
-        }
-
-        @Override
-        public void meet(BindingSetAssignment node) {
-            bindingSetList.add(node);
-            super.meet(node);
-        }
-
-    }
-    
-    
-    
-    public static class QueryNodeCount extends QueryModelVisitorBase<RuntimeException> {
-
-        private int nodeCount;
-
-        public QueryNodeCount() {
-            nodeCount = 0;
-        }
-
-        public int getNodeCount() {
-            return nodeCount;
-        }
-
-
-        @Override
-        public void meet(StatementPattern node) {
-            nodeCount += 1;
-            return;
-        }
-
-        @Override
-        public void meet(Filter node) {
-            nodeCount += 1;
-            node.getArg().visit(this);
-        }
-
-    }
-
-   
-   
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/IndexListPruner.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/IndexListPruner.java b/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/IndexListPruner.java
deleted file mode 100644
index fa1dc13..0000000
--- a/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/IndexListPruner.java
+++ /dev/null
@@ -1,35 +0,0 @@
-package mvm.rya.indexing.IndexPlanValidator;
-
-/*
- * 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 java.util.List;
-
-
-
-import java.util.Set;
-
-import mvm.rya.indexing.external.tupleSet.ExternalTupleSet;
-
-public interface IndexListPruner {
-
-    public Set<ExternalTupleSet> getRelevantIndices(List<ExternalTupleSet> indexList);
-        
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/IndexPlanValidator.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/IndexPlanValidator.java b/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/IndexPlanValidator.java
deleted file mode 100644
index 74df958..0000000
--- a/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/IndexPlanValidator.java
+++ /dev/null
@@ -1,210 +0,0 @@
-package mvm.rya.indexing.IndexPlanValidator;
-
-/*
- * 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 java.util.Iterator;
-import java.util.NoSuchElementException;
-import java.util.Set;
-
-import mvm.rya.indexing.external.tupleSet.ExternalTupleSet;
-
-import org.openrdf.query.algebra.BindingSetAssignment;
-import org.openrdf.query.algebra.Filter;
-import org.openrdf.query.algebra.Join;
-import org.openrdf.query.algebra.Projection;
-import org.openrdf.query.algebra.StatementPattern;
-import org.openrdf.query.algebra.TupleExpr;
-import org.openrdf.query.algebra.helpers.QueryModelVisitorBase;
-
-import com.google.common.collect.Sets;
-
-
-
-
-public class IndexPlanValidator implements TupleValidator {
-
-    private boolean omitCrossProd = false;
-
-    
-    public IndexPlanValidator(boolean omitCrossProd) {
-        this.omitCrossProd = omitCrossProd;
-    }
-    
-    public void setOmitCrossProd(boolean omitCrossProd) {
-        this.omitCrossProd = omitCrossProd;
-    }
-    
-    
-    @Override
-    public boolean isValid(TupleExpr te) {
-
-        TupleValidateVisitor tv = new TupleValidateVisitor();
-        te.visit(tv);
-
-        return tv.isValid();
-    }
-
-    
-    
-   
-    public int getValidTupleSize(Iterator<TupleExpr> iter) {
-        
-        int size = 0;
-        
-        while(iter.hasNext()) {
-            if(isValid(iter.next())) {
-                size++;
-            }
-        }
-        
-        return size;
-        
-    }
-    
-    
-    
-    @Override
-    public Iterator<TupleExpr> getValidTuples(Iterator<TupleExpr> tupleIter) {
-
-        final Iterator<TupleExpr> iter = tupleIter;
-        
-        return new Iterator<TupleExpr>() {
-
-            private TupleExpr next = null;
-            private boolean hasNextCalled = false;
-            private boolean isEmpty = false;
-
-            @Override
-            public boolean hasNext() {
-
-                if (!hasNextCalled && !isEmpty) {
-                    while (iter.hasNext()) {
-                        TupleExpr temp = iter.next();
-                        if (isValid(temp)) {
-                            next = temp;
-                            hasNextCalled = true;
-                            return true;
-                        }
-                    }
-                    isEmpty = true;
-                    return false;
-                } else if(isEmpty) {
-                    return false;
-                }else {
-                    return true;
-                }
-            }
-
-            @Override
-            public TupleExpr next() {
-
-                if (hasNextCalled) {
-                    hasNextCalled = false;
-                    return next;
-                } else if(isEmpty) {
-                    throw new NoSuchElementException();
-                }else {
-                    if (this.hasNext()) {
-                        hasNextCalled = false;
-                        return next;
-                    } else {
-                        throw new NoSuchElementException();
-                    }
-                }
-            }
-
-            @Override
-            public void remove() {
-
-                throw new UnsupportedOperationException("Cannot delete from iterator!");
-
-            }
-
-        };
-    }
-
-    private boolean isJoinValid(Join join) {
-
-        Set<String> leftBindingNames = join.getLeftArg().getBindingNames();
-        Set<String> rightBindingNames = join.getRightArg().getBindingNames();
-
-        
-        //System.out.println("Left binding names are " + leftBindingNames + " and right binding names are " + rightBindingNames);
-        
-        if (Sets.intersection(leftBindingNames, rightBindingNames).size() == 0) {
-            if (omitCrossProd) {
-                return false;
-            } else {
-                return true;
-            }
-
-        } else {
-            if (join.getRightArg() instanceof ExternalTupleSet) {
-
-                return ((ExternalTupleSet) join.getRightArg()).supportsBindingSet(leftBindingNames);
-
-            } else {
-                return true;
-            }
-        }
-
-    }
-
-    public class TupleValidateVisitor extends QueryModelVisitorBase<RuntimeException> {
-
-        private boolean isValid = true;
-
-        public boolean isValid() {
-            return isValid;
-        }
-
-        @Override
-        public void meet(Projection node) {
-            node.getArg().visit(this);
-        }
-
-        @Override
-        public void meet(StatementPattern node) {
-            return;
-        }
-
-        public void meet(BindingSetAssignment node) {
-            return;
-        }
-
-        @Override
-        public void meet(Filter node) {
-            node.getArg().visit(this);
-        }
-
-        @Override
-        public void meet(Join node) {
-            if (isJoinValid(node)) {
-                super.meet(node);
-            } else {
-                isValid = false;
-                return;
-            }
-        }
-
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/IndexTupleGenerator.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/IndexTupleGenerator.java b/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/IndexTupleGenerator.java
deleted file mode 100644
index 3586a5e..0000000
--- a/extras/indexing/src/main/java/mvm/rya/indexing/IndexPlanValidator/IndexTupleGenerator.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package mvm.rya.indexing.IndexPlanValidator;
-
-/*
- * 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 java.util.Iterator;
-
-import org.openrdf.query.algebra.TupleExpr;
-
-public interface IndexTupleGenerator {
-    
-    
-    public Iterator<TupleExpr> getPlans(Iterator<TupleExpr> indexPlans);
-    
-
-}



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