1.1 --- a/endpoint/pom.xml	Tue Jun 19 18:18:27 2012 +0300
     1.2 +++ b/endpoint/pom.xml	Tue Jun 19 18:23:47 2012 +0300
     1.3 @@ -100,6 +100,12 @@
     1.4  		<dependency>
     1.5  			<groupId>org.apache.cxf</groupId>
     1.6  			<artifactId>cxf-rt-transports-http-jetty</artifactId>
     1.7 +			<exclusions>
     1.8 +				<exclusion>
     1.9 +					<artifactId>slf4j-jdk14</artifactId>
    1.10 +					<groupId>org.slf4j</groupId>
    1.11 +				</exclusion>
    1.12 +			</exclusions>
    1.13  		</dependency>
    1.14  
    1.15  		<dependency>

     2.1 --- a/evaluation/pom.xml	Tue Jun 19 18:18:27 2012 +0300
     2.2 +++ b/evaluation/pom.xml	Tue Jun 19 18:23:47 2012 +0300
     2.3 @@ -32,26 +32,10 @@
     2.4  
     2.5  		<dependency>
     2.6  			<groupId>org.slf4j</groupId>
     2.7 -			<artifactId>slf4j-api</artifactId>
     2.8 -		</dependency>
     2.9 -
    2.10 -		<!-- 
    2.11 -		<dependency>
    2.12 -			<groupId>org.slf4j</groupId>
    2.13 -			<artifactId>slf4j-simple</artifactId>
    2.14 -		</dependency>
    2.15 -		-->
    2.16 -		<dependency>
    2.17 -			<groupId>org.slf4j</groupId>
    2.18  			<artifactId>slf4j-log4j12</artifactId>
    2.19  		</dependency>
    2.20  
    2.21  		<dependency>
    2.22 -			<groupId>log4j</groupId>
    2.23 -			<artifactId>log4j</artifactId>
    2.24 -		</dependency>
    2.25 -
    2.26 -		<dependency>
    2.27  			<groupId>junit</groupId>
    2.28  			<artifactId>junit</artifactId>
    2.29  		</dependency>

     3.1 --- a/evaluation/src/main/java/org/openrdf/query/algebra/evaluation/impl/SpatialJoinOptimizer.java	Tue Jun 19 18:18:27 2012 +0300
     3.2 +++ b/evaluation/src/main/java/org/openrdf/query/algebra/evaluation/impl/SpatialJoinOptimizer.java	Tue Jun 19 18:23:47 2012 +0300
     3.3 @@ -52,7 +52,9 @@
     3.4   * @author James Leigh
     3.5   */
     3.6  
     3.7 -public class SpatialJoinOptimizer implements QueryOptimizer {
     3.8 +public class SpatialJoinOptimizer 
     3.9 +//implements QueryOptimizer //Removed it consciously 
    3.10 +{
    3.11  
    3.12  
    3.13  	//private Set<String> existingVars = new TreeSet<String>();
    3.14 @@ -62,12 +64,21 @@
    3.15  	 * 
    3.16  	 * @param tupleExpr
    3.17  	 */
    3.18 -	public void optimize(TupleExpr tupleExpr, Dataset dataset, BindingSet bindings) {
    3.19 -		tupleExpr.visit(new JoinVisitor());
    3.20 +	public void optimize(TupleExpr tupleExpr, Dataset dataset, BindingSet bindings, List<TupleExpr> spatialJoins) {
    3.21 +		tupleExpr.visit(new JoinVisitor(spatialJoins));
    3.22  	}
    3.23  
    3.24  	protected class JoinVisitor extends QueryModelVisitorBase<RuntimeException> {
    3.25 +		
    3.26 +		
    3.27 +		
    3.28 +		public JoinVisitor(List<TupleExpr> spatialJoins) {
    3.29 +			super();
    3.30 +			this.spatialJoins = spatialJoins;
    3.31 +		}
    3.32  
    3.33 +		
    3.34 +		private List<TupleExpr> spatialJoins;
    3.35  		//buffer with a var as a second argument
    3.36  		private boolean problematicBuffer = false;
    3.37  
    3.38 @@ -275,6 +286,9 @@
    3.39  							Map.Entry entry = (Map.Entry)it.next();
    3.40  							if(count == position - varsMapSize)
    3.41  							{
    3.42 +								//If I keep record of this entry, I can use the info later to avoid duplicate filters
    3.43 +								spatialJoins.add((TupleExpr) entry.getKey());
    3.44 +								//
    3.45  								orderedJoinArgs.add((TupleExpr) entry.getKey());
    3.46  								it.remove();
    3.47  								for(int fix = 0 ; fix < finalList.size(); fix++)
    3.48 @@ -329,7 +343,11 @@
    3.49  			}
    3.50  		}
    3.51  
    3.52 -
    3.53 +		/**
    3.54 +		 * General Comment: If more than one function exists in the query and can be used to perform the join, no preference is shown 
    3.55 +		 * on which function will actually be used for this purpose. This could cause an issue if ST_Disjoint is the one finally used, 
    3.56 +		 * as the index won't be used for the evaluation in this case. Perhaps I should include some 'priority'
    3.57 +		 */
    3.58  		@Override
    3.59  		public void meet(Filter node) {
    3.60  

     4.1 --- a/generaldb/pom.xml	Tue Jun 19 18:18:27 2012 +0300
     4.2 +++ b/generaldb/pom.xml	Tue Jun 19 18:23:47 2012 +0300
     4.3 @@ -63,11 +63,6 @@
     4.4  		</dependency>
     4.5  
     4.6  		<dependency>
     4.7 -			<groupId>org.slf4j</groupId>
     4.8 -			<artifactId>slf4j-api</artifactId>
     4.9 -		</dependency>
    4.10 -
    4.11 -		<dependency>
    4.12  			<groupId>commons-dbcp</groupId>
    4.13  			<artifactId>commons-dbcp</artifactId>
    4.14  		</dependency>

     5.1 --- a/generaldb/src/main/java/org/openrdf/sail/generaldb/optimizers/GeneralDBQueryOptimizer.java	Tue Jun 19 18:18:27 2012 +0300
     5.2 +++ b/generaldb/src/main/java/org/openrdf/sail/generaldb/optimizers/GeneralDBQueryOptimizer.java	Tue Jun 19 18:23:47 2012 +0300
     5.3 @@ -5,6 +5,9 @@
     5.4   */
     5.5  package org.openrdf.sail.generaldb.optimizers;
     5.6  
     5.7 +import java.util.ArrayList;
     5.8 +import java.util.List;
     5.9 +
    5.10  import org.openrdf.query.BindingSet;
    5.11  import org.openrdf.query.Dataset;
    5.12  import org.openrdf.query.algebra.QueryRoot;
    5.13 @@ -42,7 +45,11 @@
    5.14  	private GeneralDBSelectQueryOptimizerFactory factory;
    5.15  
    5.16  	private HashTable hashTable;
    5.17 -
    5.18 +	
    5.19 +	//Addition to locate duplicate filters caused by the SpatialJoinOptimizer
    5.20 +	List<TupleExpr> spatialJoins = new ArrayList<TupleExpr>();
    5.21 +	//
    5.22 +	
    5.23  	public void setSelectQueryOptimizerFactory(GeneralDBSelectQueryOptimizerFactory factory) {
    5.24  		this.factory = factory;
    5.25  	}
    5.26 @@ -100,12 +107,13 @@
    5.27  		new SameTermFilterOptimizer().optimize(expr, dataset, bindings);
    5.28  
    5.29  		//XXX
    5.30 -		new SpatialJoinOptimizer().optimize(expr, dataset, bindings);
    5.31 +		new SpatialJoinOptimizer().optimize(expr, dataset, bindings,spatialJoins);
    5.32  	}
    5.33  
    5.34  	protected void rdbmsOptimizations(TupleExpr expr, Dataset dataset, BindingSet bindings) {
    5.35  		new GeneralDBValueIdLookupOptimizer(vf).optimize(expr, dataset, bindings);
    5.36 -		factory.createRdbmsFilterOptimizer().optimize(expr, dataset, bindings);
    5.37 +		factory.createRdbmsFilterOptimizer().optimize(expr, dataset, bindings,spatialJoins);
    5.38 +		this.spatialJoins.clear();
    5.39  		new GeneralDBVarColumnLookupOptimizer().optimize(expr, dataset, bindings);
    5.40  		GeneralDBValueJoinOptimizer valueJoins = new GeneralDBValueJoinOptimizer();
    5.41  		valueJoins.setBnodeTable(bnodes);

     6.1 --- a/generaldb/src/main/java/org/openrdf/sail/generaldb/optimizers/GeneralDBSelectQueryOptimizer.java	Tue Jun 19 18:18:27 2012 +0300
     6.2 +++ b/generaldb/src/main/java/org/openrdf/sail/generaldb/optimizers/GeneralDBSelectQueryOptimizer.java	Tue Jun 19 18:23:47 2012 +0300
     6.3 @@ -52,6 +52,7 @@
     6.4  import org.openrdf.query.algebra.Projection;
     6.5  import org.openrdf.query.algebra.ProjectionElem;
     6.6  import org.openrdf.query.algebra.ProjectionElemList;
     6.7 +import org.openrdf.query.algebra.QueryModelNode;
     6.8  import org.openrdf.query.algebra.Slice;
     6.9  import org.openrdf.query.algebra.StatementPattern;
    6.10  import org.openrdf.query.algebra.TupleExpr;
    6.11 @@ -113,16 +114,17 @@
    6.12   * @author James Leigh
    6.13   * 
    6.14   */
    6.15 -public class GeneralDBSelectQueryOptimizer extends GeneralDBQueryModelVisitorBase<RuntimeException> implements
    6.16 -QueryOptimizer
    6.17 +public class GeneralDBSelectQueryOptimizer extends GeneralDBQueryModelVisitorBase<RuntimeException> 
    6.18 +//implements QueryOptimizer //removed it consciously
    6.19  {
    6.20  
    6.21  	/**
    6.22  	 * XXX additions (manolee)
    6.23  	 */
    6.24 +	private List<TupleExpr> spatialJoins;
    6.25  
    6.26  	//assuming no more than 10 uniquely-named variables will be spatial in the average case 
    6.27 -	private ArrayList<String> geoNames = new ArrayList<String>(10);
    6.28 +	private List<String> geoNames = new ArrayList<String>(10);
    6.29  
    6.30  	//private Map<String, GeneralDBSqlExpr> constructsForSelect = new HashMap<String, GeneralDBSqlExpr>();
    6.31  
    6.32 @@ -183,29 +185,29 @@
    6.33  		this.ids = ids;
    6.34  	}
    6.35  
    6.36 -	public void optimize(TupleExpr tupleExpr, Dataset dataset, BindingSet bindings) {
    6.37 +	public void optimize(TupleExpr tupleExpr, Dataset dataset, BindingSet bindings, List<TupleExpr> spatialJoins) {
    6.38  		this.dataset = dataset;
    6.39  		this.bindings = bindings;
    6.40 +		this.spatialJoins = spatialJoins;
    6.41  		tupleExpr.visit(this);
    6.42 -		//System.out.println("placeholder");
    6.43  	}
    6.44  
    6.45  	@Override
    6.46  	public void meet(Distinct node)
    6.47 -	throws RuntimeException
    6.48 -	{
    6.49 +			throws RuntimeException
    6.50 +			{
    6.51  		super.meet(node);
    6.52  		if (node.getArg() instanceof GeneralDBSelectQuery) {
    6.53  			GeneralDBSelectQuery query = (GeneralDBSelectQuery)node.getArg();
    6.54  			query.setDistinct(true);
    6.55  			node.replaceWith(query);
    6.56  		}
    6.57 -	}
    6.58 +			}
    6.59  
    6.60  	@Override
    6.61  	public void meet(Union node)
    6.62 -	throws RuntimeException
    6.63 -	{
    6.64 +			throws RuntimeException
    6.65 +			{
    6.66  		super.meet(node);
    6.67  		TupleExpr l = node.getLeftArg();
    6.68  		TupleExpr r = node.getRightArg();
    6.69 @@ -225,7 +227,7 @@
    6.70  		mergeSelectClause(query, right);
    6.71  		addProjectionsFromUnion(query, union);
    6.72  		node.replaceWith(query);
    6.73 -	}
    6.74 +			}
    6.75  
    6.76  	/**
    6.77  	 * This happens when both sides of the union have the same variable name with
    6.78 @@ -248,8 +250,8 @@
    6.79  
    6.80  	@Override
    6.81  	public void meet(Join node)
    6.82 -	throws RuntimeException
    6.83 -	{
    6.84 +			throws RuntimeException
    6.85 +			{
    6.86  		super.meet(node);
    6.87  		TupleExpr l = node.getLeftArg();
    6.88  		TupleExpr r = node.getRightArg();
    6.89 @@ -270,12 +272,12 @@
    6.90  		 * This change was made before altering the spatial joins operation
    6.91  		 */
    6.92  		reference = left;
    6.93 -	}
    6.94 +			}
    6.95  
    6.96  	@Override
    6.97  	public void meet(LeftJoin node)
    6.98 -	throws RuntimeException
    6.99 -	{
   6.100 +			throws RuntimeException
   6.101 +			{
   6.102  		super.meet(node);
   6.103  		TupleExpr l = node.getLeftArg();
   6.104  		TupleExpr r = node.getRightArg();
   6.105 @@ -306,7 +308,7 @@
   6.106  		}
   6.107  		node.replaceWith(left);
   6.108  		reference = left;
   6.109 -	}
   6.110 +			}
   6.111  
   6.112  	@Override
   6.113  	public void meet(StatementPattern sp) {
   6.114 @@ -497,8 +499,8 @@
   6.115  
   6.116  	@Override
   6.117  	public void meet(Filter node)
   6.118 -	throws RuntimeException
   6.119 -	{
   6.120 +			throws RuntimeException
   6.121 +			{
   6.122  
   6.123  		/**
   6.124  		 * XXX 21/09/2011 addition for spatial joins
   6.125 @@ -752,40 +754,69 @@
   6.126  		/**
   6.127  		 * End of addition
   6.128  		 */
   6.129 -		else //DEFAULT BEHAVIOR
   6.130 +		else //DEFAULT BEHAVIOR (Enhanced with check for duplicates)
   6.131  		{
   6.132 +
   6.133 +			boolean dup = false;
   6.134 +			ValueExpr dupFunctionCall = node.getCondition();
   6.135 +			for(TupleExpr sfilter : this.spatialJoins)
   6.136 +			{
   6.137 +				ValueExpr tmpExpr = ((Filter)sfilter).getCondition();
   6.138 +				if(tmpExpr.equals(dupFunctionCall))
   6.139 +				{
   6.140 +					//					QueryModelNode parent = node.getParentNode();
   6.141 +					//					TupleExpr replacement = ((Filter)node).getArg();
   6.142 +					//					parent.replaceChildNode(node, replacement);
   6.143 +					//					//If I do reach this point, the former 'child' argument will be a traditional Join operator
   6.144 +					//					super.meet((Join)replacement);
   6.145 +					//					node.setCondition(null);
   6.146 +					//					return;
   6.147 +					dup = true;
   6.148 +					break;
   6.149 +				}
   6.150 +			}
   6.151 +
   6.152  			super.meet(node);
   6.153  			if (node.getArg() instanceof GeneralDBSelectQuery) {
   6.154  				GeneralDBSelectQuery query = (GeneralDBSelectQuery)node.getArg();
   6.155  
   6.156  				ValueExpr condition = null;
   6.157 -				for (ValueExpr expr : flatten(node.getCondition())) {
   6.158 -					try {
   6.159 -						//07/09/2011
   6.160 -						//Attempt to move spatial selections and joins to FROM clause
   6.161 -						//XXX removed because I followed a different approach. May come in handy later on. 09/09/11
   6.162 -						//					if(node.getCondition() instanceof FunctionCall)
   6.163 -						//					{
   6.164 -						//						GeneralDBSqlExpr sqlExpression = sql.createBooleanExpr(expr);
   6.165 -						//						query.addSpatialFilter(sqlExpression);
   6.166 -						//						//query.getFrom().addFilter(sql.createBooleanExpr(expr));
   6.167 -						//						query.addFilter(sqlExpression);
   6.168 -						//					}
   6.169 -						//					else //DEFAULT CASE
   6.170 -						//					{
   6.171 -						query.addFilter(sql.createBooleanExpr(expr));
   6.172 -						//					}
   6.173 +//				dup=false;
   6.174 +				if(!dup)
   6.175 +				{
   6.176 +					for (ValueExpr expr : flatten(node.getCondition())) {
   6.177 +						try {
   6.178 +							//07/09/2011
   6.179 +							//Attempt to move spatial selections and joins to FROM clause
   6.180 +							//XXX removed because I followed a different approach. May come in handy later on. 09/09/11
   6.181 +							//					if(node.getCondition() instanceof FunctionCall)
   6.182 +							//					{
   6.183 +							//						GeneralDBSqlExpr sqlExpression = sql.createBooleanExpr(expr);
   6.184 +							//						query.addSpatialFilter(sqlExpression);
   6.185 +							//						//query.getFrom().addFilter(sql.createBooleanExpr(expr));
   6.186 +							//						query.addFilter(sqlExpression);
   6.187 +							//					}
   6.188 +							//					else //DEFAULT CASE
   6.189 +							//					{
   6.190 +							query.addFilter(sql.createBooleanExpr(expr));
   6.191 +							//					}
   6.192  
   6.193 -					}
   6.194 -					catch (UnsupportedRdbmsOperatorException e) {
   6.195 -						if (condition == null) {
   6.196 -							condition = expr;
   6.197  						}
   6.198 -						else {
   6.199 -							condition = new And(condition, expr);
   6.200 +						catch (UnsupportedRdbmsOperatorException e) {
   6.201 +							if (condition == null) {
   6.202 +								condition = expr;
   6.203 +							}
   6.204 +							else {
   6.205 +								condition = new And(condition, expr);
   6.206 +							}
   6.207  						}
   6.208  					}
   6.209  				}
   6.210 +				else
   6.211 +				{
   6.212 +					condition = null;
   6.213 +				}
   6.214 +
   6.215  				if (condition == null) {
   6.216  					node.replaceWith(node.getArg());
   6.217  				}
   6.218 @@ -838,14 +869,14 @@
   6.219  
   6.220  
   6.221  		}
   6.222 -	}
   6.223 +			}
   6.224  
   6.225  
   6.226  
   6.227  	@Override
   6.228  	public void meet(Projection node)
   6.229 -	throws RuntimeException
   6.230 -	{
   6.231 +			throws RuntimeException
   6.232 +			{
   6.233  		super.meet(node);
   6.234  		if (node.getArg() instanceof GeneralDBSelectQuery) {
   6.235  			GeneralDBSelectQuery query = (GeneralDBSelectQuery)node.getArg();
   6.236 @@ -866,15 +897,15 @@
   6.237  			query.setSqlSelectVar(selection);
   6.238  			node.replaceWith(query);
   6.239  		}
   6.240 -	}
   6.241 +			}
   6.242  
   6.243  	/**
   6.244  	 * XXX used to retrieve the geoNames from the TRADITIONAL filter clauses - not the ones in Joins
   6.245  	 */
   6.246  	@Override
   6.247  	public void meet(FunctionCall node)
   6.248 -	throws RuntimeException
   6.249 -	{
   6.250 +			throws RuntimeException
   6.251 +			{
   6.252  		Function function = FunctionRegistry.getInstance().get(node.getURI());
   6.253  
   6.254  		super.meet(node);
   6.255 @@ -936,7 +967,7 @@
   6.256  			//			}
   6.257  		}
   6.258  
   6.259 -	}
   6.260 +			}
   6.261  
   6.262  	//
   6.263  	@Override
   6.264 @@ -1042,7 +1073,7 @@
   6.265  		else if(expr instanceof BinaryValueOperator)
   6.266  		{
   6.267  			return thematicExpression(((BinaryValueOperator) expr).getLeftArg()) &&
   6.268 -				   thematicExpression(((BinaryValueOperator) expr).getRightArg());
   6.269 +					thematicExpression(((BinaryValueOperator) expr).getRightArg());
   6.270  		}
   6.271  		else
   6.272  		{
   6.273 @@ -1195,8 +1226,8 @@
   6.274  
   6.275  	@Override
   6.276  	public void meet(Slice node)
   6.277 -	throws RuntimeException
   6.278 -	{
   6.279 +			throws RuntimeException
   6.280 +			{
   6.281  		super.meet(node);
   6.282  		if (node.getArg() instanceof GeneralDBSelectQuery) {
   6.283  			GeneralDBSelectQuery query = (GeneralDBSelectQuery)node.getArg();
   6.284 @@ -1208,12 +1239,12 @@
   6.285  			}
   6.286  			node.replaceWith(query);
   6.287  		}
   6.288 -	}
   6.289 +			}
   6.290  
   6.291  	@Override
   6.292  	public void meet(Order node)
   6.293 -	throws RuntimeException
   6.294 -	{
   6.295 +			throws RuntimeException
   6.296 +			{
   6.297  		int mbbCounter = 0;
   6.298  		//		super.meet(node);
   6.299  		if (!(node.getArg() instanceof GeneralDBSelectQuery))
   6.300 @@ -1344,7 +1375,7 @@
   6.301  		catch (UnsupportedRdbmsOperatorException e) {
   6.302  			// unsupported
   6.303  		}
   6.304 -	}
   6.305 +			}
   6.306  
   6.307  	/**
   6.308  	 * FIXME uncomment if you need sorted results based on the group by's contents!!!

     7.1 --- a/monetdb/pom.xml	Tue Jun 19 18:18:27 2012 +0300
     7.2 +++ b/monetdb/pom.xml	Tue Jun 19 18:23:47 2012 +0300
     7.3 @@ -67,11 +67,6 @@
     7.4  		</dependency>
     7.5  
     7.6  		<dependency>
     7.7 -			<groupId>org.slf4j</groupId>
     7.8 -			<artifactId>slf4j-api</artifactId>
     7.9 -		</dependency>
    7.10 -
    7.11 -		<dependency>
    7.12  			<groupId>commons-dbcp</groupId>
    7.13  			<artifactId>commons-dbcp</artifactId>
    7.14  		</dependency>

     8.1 --- a/pom.xml	Tue Jun 19 18:18:27 2012 +0300
     8.2 +++ b/pom.xml	Tue Jun 19 18:23:47 2012 +0300
     8.3 @@ -33,7 +33,6 @@
     8.4  		<sesame.version>2.6.3</sesame.version>
     8.5  		<aduna.appbase.version>3.5.0</aduna.appbase.version>
     8.6  		<slf4j.version>1.6.4</slf4j.version>
     8.7 -		<log4j.version>1.2.17</log4j.version>
     8.8  		<spring.version>2.5.6</spring.version>
     8.9  		<jts.version>1.11</jts.version>
    8.10  		<geotools.version>2.7.4</geotools.version>
    8.11 @@ -318,21 +317,6 @@
    8.12  				<version>5.1.15</version>
    8.13  			</dependency>
    8.14  
    8.15 -			<!-- SLF4J -->
    8.16 -			<dependency>
    8.17 -				<groupId>org.slf4j</groupId>
    8.18 -				<artifactId>slf4j-api</artifactId>
    8.19 -				<version>${slf4j.version}</version>
    8.20 -			</dependency>
    8.21 -
    8.22 -			<!-- 
    8.23 -			<dependency>
    8.24 -				<groupId>org.slf4j</groupId>
    8.25 -				<artifactId>slf4j-simple</artifactId>
    8.26 -				<version>${slf4j.version}</version>
    8.27 -			</dependency>
    8.28 -   			-->
    8.29 -   			
    8.30  			<dependency>
    8.31  				<groupId>net.sf</groupId>
    8.32  				<artifactId>log4jdbc4</artifactId>
    8.33 @@ -346,13 +330,6 @@
    8.34  				<version>${slf4j.version}</version>
    8.35  			</dependency>
    8.36  			
    8.37 -			<dependency>
    8.38 -				<groupId>log4j</groupId>
    8.39 -				<artifactId>log4j</artifactId>
    8.40 -				<version>${log4j.version}</version>
    8.41 -			</dependency>
    8.42 -			            
    8.43 -			
    8.44  			<!-- Apache Commons -->
    8.45  			<dependency>
    8.46  				<groupId>commons-cli</groupId>

     9.1 --- a/postgis/pom.xml	Tue Jun 19 18:18:27 2012 +0300
     9.2 +++ b/postgis/pom.xml	Tue Jun 19 18:23:47 2012 +0300
     9.3 @@ -67,11 +67,6 @@
     9.4  		</dependency>
     9.5  
     9.6  		<dependency>
     9.7 -			<groupId>org.slf4j</groupId>
     9.8 -			<artifactId>slf4j-api</artifactId>
     9.9 -		</dependency>
    9.10 -
    9.11 -		<dependency>
    9.12  			<groupId>commons-dbcp</groupId>
    9.13  			<artifactId>commons-dbcp</artifactId>
    9.14  		</dependency>

    10.1 --- a/postgis/src/main/java/org/openrdf/sail/postgis/evaluation/PostGISEvaluation.java	Tue Jun 19 18:18:27 2012 +0300
    10.2 +++ b/postgis/src/main/java/org/openrdf/sail/postgis/evaluation/PostGISEvaluation.java	Tue Jun 19 18:23:47 2012 +0300
    10.3 @@ -64,6 +64,7 @@
    10.4  					stmt.setObject(++p, o);
    10.5  				}
    10.6  				Collection<GeneralDBColumnVar> proj = qb.getProjections();
    10.7 +//				System.out.println("In PostGIS Evaluation, query is: \n" + stmt);
    10.8  				GeneralDBBindingIteration result = new PostGISBindingIteration(stmt);
    10.9  				result.setProjections(proj);
   10.10  				result.setBindings(bindings);
   10.11 @@ -72,8 +73,7 @@
   10.12  				//XXX addition
   10.13  				result.setGeoNames(this.geoNames);
   10.14  				result.setConstructIndexesAndNames(this.constructIndexesAndNames);
   10.15 -				//
   10.16 -		
   10.17 +				
   10.18  				if (logger.isDebugEnabled()) {
   10.19  					logger.debug("In PostGIS Evaluation, query is: \n{}", stmt);
   10.20  				}

    11.1 --- a/resultio/pom.xml	Tue Jun 19 18:18:27 2012 +0300
    11.2 +++ b/resultio/pom.xml	Tue Jun 19 18:23:47 2012 +0300
    11.3 @@ -49,24 +49,8 @@
    11.4  
    11.5  		<dependency>
    11.6  			<groupId>org.slf4j</groupId>
    11.7 -			<artifactId>slf4j-api</artifactId>
    11.8 -		</dependency>
    11.9 -		
   11.10 -		<!-- 		
   11.11 -		<dependency>
   11.12 -			<groupId>org.slf4j</groupId>
   11.13 -			<artifactId>slf4j-simple</artifactId>
   11.14 -		</dependency>
   11.15 -		-->
   11.16 -		<dependency>
   11.17 -			<groupId>org.slf4j</groupId>
   11.18  			<artifactId>slf4j-log4j12</artifactId>
   11.19  		</dependency>
   11.20 -
   11.21 -		<dependency>
   11.22 -			<groupId>log4j</groupId>
   11.23 -			<artifactId>log4j</artifactId>
   11.24 -		</dependency>
   11.25  		
   11.26  		<dependency>
   11.27  			<groupId>junit</groupId>

    12.1 --- a/runtime/log4j.properties	Tue Jun 19 18:18:27 2012 +0300
    12.2 +++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
    12.3 @@ -1,22 +0,0 @@
    12.4 -# logger level values: OFF, ERROR, WARN, INFO, DEBUG, ALL
    12.5 -log4j.rootLogger=OFF, CA
    12.6 -#log4j.rootLogger=DEBUG, CA
    12.7 -#log4j.rootLogger=INFO, CA, FA
    12.8 -
    12.9 -# Console Appender
   12.10 -log4j.appender.CA=org.apache.log4j.ConsoleAppender
   12.11 -log4j.appender.CA.layout=org.apache.log4j.PatternLayout
   12.12 -log4j.appender.CA.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
   12.13 -
   12.14 -# File Appender
   12.15 -#log4j.appender.FA=org.apache.log4j.FileAppender
   12.16 -#log4j.appender.FA.File=sample.log
   12.17 -#log4j.appender.FA.layout=org.apache.log4j.PatternLayout
   12.18 -#log4j.appender.FA.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
   12.19 -# Set the logger level of File Appender to WARN
   12.20 -#log4j.appender.FA.Threshold = WARN
   12.21 -
   12.22 -
   12.23 -# Sesame configuration (debug only Strabon)
   12.24 -log4j.logger.org.openrdf.query.parser.QueryParserRegistry=INFO
   12.25 -log4j.logger.org.openrdf.sail.generaldb.managers.TripleTableManager=INFO

    13.1 --- a/runtime/src/main/java/eu/earthobservatory/runtime/generaldb/Strabon.java	Tue Jun 19 18:18:27 2012 +0300
    13.2 +++ b/runtime/src/main/java/eu/earthobservatory/runtime/generaldb/Strabon.java	Tue Jun 19 18:23:47 2012 +0300
    13.3 @@ -90,14 +90,14 @@
    13.4  	SailRepositoryConnection con1 = null;
    13.5  
    13.6  	public Strabon(String databaseName, String user, String password, int port, String serverName, boolean checkForLockTable) 
    13.7 -	throws SQLException, ClassNotFoundException 
    13.8 -	{
    13.9 +			throws SQLException, ClassNotFoundException 
   13.10 +			{
   13.11  		if (checkForLockTable == true) {
   13.12  			checkAndDeleteLock(databaseName, user, password, port, serverName);
   13.13  		}
   13.14  
   13.15  		initiate(databaseName, user, password, port, serverName);
   13.16 -	}
   13.17 +			}
   13.18  
   13.19  
   13.20  	protected abstract void initiate(String databaseName, String user, String password, int port, String serverName) ;
   13.21 @@ -128,7 +128,7 @@
   13.22  
   13.23  
   13.24  	protected abstract void checkAndDeleteLock(String databaseName, String user, String password, int port, String serverName)
   13.25 -	throws SQLException, ClassNotFoundException ;
   13.26 +			throws SQLException, ClassNotFoundException ;
   13.27  
   13.28  	public SailRepositoryConnection getSailRepoConnection() {
   13.29  		return con1;
   13.30 @@ -145,31 +145,31 @@
   13.31  			con1.commit();
   13.32  			con1.close();
   13.33  			repo1.shutDown();
   13.34 -			
   13.35 +
   13.36  		} catch (RepositoryException e) {
   13.37  			logger.error("[Strabon.close]", e);
   13.38  		}
   13.39 -		
   13.40 +
   13.41  		logger.info("[Strabon.close] Connection closed.");
   13.42  	}
   13.43  
   13.44  	public Object query(String queryString)
   13.45 -	throws  MalformedQueryException, QueryEvaluationException, IOException, TupleQueryResultHandlerException
   13.46 -	{
   13.47 +			throws  MalformedQueryException, QueryEvaluationException, IOException, TupleQueryResultHandlerException
   13.48 +			{
   13.49  		return query(queryString, "", this.getSailRepoConnection());	
   13.50 -	}
   13.51 +			}
   13.52  
   13.53  	public Object query(String queryString, String resultsFormat)
   13.54 -	throws  MalformedQueryException , QueryEvaluationException, IOException, TupleQueryResultHandlerException
   13.55 -	{
   13.56 +			throws  MalformedQueryException , QueryEvaluationException, IOException, TupleQueryResultHandlerException
   13.57 +			{
   13.58  		return query(queryString, resultsFormat, this.getSailRepoConnection());
   13.59 -	}
   13.60 +			}
   13.61  
   13.62  	public Object query(String queryString, SailRepositoryConnection con)
   13.63 -	throws  MalformedQueryException, QueryEvaluationException, IOException, TupleQueryResultHandlerException
   13.64 -	{
   13.65 +			throws  MalformedQueryException, QueryEvaluationException, IOException, TupleQueryResultHandlerException
   13.66 +			{
   13.67  		return query(queryString, "", con);	
   13.68 -	}
   13.69 +			}
   13.70  
   13.71  	public Object queryBindings(String queryString, SailRepositoryConnection con) throws QueryEvaluationException, MalformedQueryException
   13.72  	{
   13.73 @@ -183,10 +183,10 @@
   13.74  		TupleQueryResult result = tupleQuery.evaluate();
   13.75  		return result;
   13.76  	}
   13.77 -	
   13.78 +
   13.79  	public Object query(String queryString, String resultsFormat, SailRepositoryConnection con)
   13.80 -	throws  MalformedQueryException, QueryEvaluationException, IOException, TupleQueryResultHandlerException 
   13.81 -	{
   13.82 +			throws  MalformedQueryException, QueryEvaluationException, IOException, TupleQueryResultHandlerException 
   13.83 +			{
   13.84  		logger.info("[Strabon.query] Executing query: " + queryString);
   13.85  		TupleQuery tupleQuery = null;
   13.86  		try {
   13.87 @@ -618,11 +618,11 @@
   13.88  			try {
   13.89  				//String cstr = new String("aa", "UTF8");
   13.90  				// ggarbis: For too large strings (e.g., 44MB) it returns empty string.
   13.91 -//				String newString = new String(sb.toString().getBytes(), Charset.availableCharsets().get("UTF-8"));
   13.92 +				//				String newString = new String(sb.toString().getBytes(), Charset.availableCharsets().get("UTF-8"));
   13.93  
   13.94  				if(resultsFormat.equalsIgnoreCase("KML"))
   13.95  				{
   13.96 -//					writeOut.write(newString);
   13.97 +					//					writeOut.write(newString);
   13.98  					writeOut.write(sb.toString());
   13.99  					//					System.out.println(newString);
  13.100  				}
  13.101 @@ -638,7 +638,7 @@
  13.102  
  13.103  					//kmzout.setLevel(6);
  13.104  					kmzout.putNextEntry(entry);
  13.105 -//					kmzout.write(newString.getBytes());
  13.106 +					//					kmzout.write(newString.getBytes());
  13.107  					kmzout.write(sb.toString().getBytes());
  13.108  					kmzout.closeEntry();
  13.109  					kmzout.close();
  13.110 @@ -764,7 +764,7 @@
  13.111  
  13.112  		//return ret;
  13.113  		return retStream.toString();
  13.114 -	}
  13.115 +			}
  13.116  
  13.117  	public void update(String updateString, SailRepositoryConnection con) throws MalformedQueryException 
  13.118  	{
  13.119 @@ -786,9 +786,9 @@
  13.120  			logger.error("[Strabon.update]", e);
  13.121  		}
  13.122  
  13.123 -//		System.out.println("-------------------------------------------");
  13.124 -//		System.out.println("-            UPDATE EXECUTED              -");
  13.125 -//		System.out.println("-------------------------------------------");
  13.126 +		//		System.out.println("-------------------------------------------");
  13.127 +		//		System.out.println("-            UPDATE EXECUTED              -");
  13.128 +		//		System.out.println("-------------------------------------------");
  13.129  	}
  13.130  
  13.131  	public void storeInRepo(String src, String format) throws RDFParseException, RepositoryException, IOException,InvalidDatasetFormatFault, RDFHandlerException
  13.132 @@ -833,21 +833,30 @@
  13.133  		{
  13.134  			throw new InvalidDatasetFormatFault();
  13.135  		}
  13.136 -		
  13.137 -       try{
  13.138 -    	   URL source = new URL(src);
  13.139 -    	   storeURL(source, baseURI, uriContext, realFormat);
  13.140 -    	   
  13.141 -       } catch(MalformedURLException e) {
  13.142 -    	   File file = new File(src);
  13.143 -    	   if (file.exists()) {
  13.144 -    		   storeURL(new URL("file://" + src), baseURI, uriContext, realFormat);
  13.145 -    		   
  13.146 -    	   } else {
  13.147 -    		   logger.info("File \"" + src + "\" does not exist. Trying reading as String.");
  13.148 -    		   storeString((String)src, baseURI, uriContext, realFormat);
  13.149 -    	   }
  13.150 -       }
  13.151 +
  13.152 +		try{
  13.153 +			URL source = new URL(src);
  13.154 +			storeURL(source, baseURI, uriContext, realFormat);
  13.155 +
  13.156 +		} catch(MalformedURLException e) {
  13.157 +
  13.158 +			URL fromClasspath = getClass().getResource(src);
  13.159 +			if(fromClasspath!=null)
  13.160 +			{
  13.161 +				storeURL(fromClasspath, baseURI, uriContext, realFormat);
  13.162 +			}
  13.163 +			else
  13.164 +			{
  13.165 +				File file = new File(src);
  13.166 +				if (file.exists()) {
  13.167 +					storeURL(new URL("file://" + src), baseURI, uriContext, realFormat);
  13.168 +
  13.169 +				} else {
  13.170 +					logger.info("File \"" + src + "\" does not exist. Trying reading as String.");
  13.171 +					storeString((String)src, baseURI, uriContext, realFormat);
  13.172 +				}
  13.173 +			}
  13.174 +		}
  13.175  	}
  13.176  
  13.177  	private void storeURL(URL url, String baseURI, URI context, RDFFormat format) throws RDFParseException, RepositoryException, IOException, RDFHandlerException
  13.178 @@ -860,14 +869,14 @@
  13.179  
  13.180  		InputStream in = (InputStream) url.openStream();
  13.181  		InputStreamReader reader = new InputStreamReader(in);
  13.182 -		
  13.183 +
  13.184  		RDFParser parser = Rio.createParser(format);
  13.185 -		
  13.186 +
  13.187  		GeosparqlRDFHandlerBase handler = new GeosparqlRDFHandlerBase();
  13.188 -		
  13.189 +
  13.190  		parser.setRDFHandler(handler);
  13.191  		parser.parse(reader, "");
  13.192 -		
  13.193 +
  13.194  		logger.info("[Strabon.storeURL] Inferred " + handler.getNumberOfTriples() + " triples.");
  13.195  		if (handler.getNumberOfTriples() > 0) {
  13.196  			logger.info("[Strabon.storeURL] Triples inferred:"+ handler.getTriples().toString());
  13.197 @@ -897,14 +906,14 @@
  13.198  		logger.info("[Strabon.storeString] Format   : " + ((format == null) ? "null" : format.toString()));
  13.199  
  13.200  		StringReader reader = new StringReader(text);
  13.201 -		
  13.202 +
  13.203  		RDFParser parser = Rio.createParser(format);
  13.204 -		
  13.205 +
  13.206  		GeosparqlRDFHandlerBase handler = new GeosparqlRDFHandlerBase();
  13.207 -		
  13.208 +
  13.209  		parser.setRDFHandler(handler);
  13.210  		parser.parse(reader, "");
  13.211 -		
  13.212 +
  13.213  		logger.info("[Strabon.storeString] Inferred " + handler.getNumberOfTriples() + " triples.");
  13.214  		if (handler.getNumberOfTriples() > 0) {
  13.215  			logger.info("[Strabon.storeString] Triples inferred:"+ handler.getTriples().toString());
  13.216 @@ -934,16 +943,16 @@
  13.217  			logger.error("[Strabon.describe]", e);
  13.218  		}
  13.219  
  13.220 -//		System.out.println("Placemark0");
  13.221 -//		System.out.println("\n\n\nGot query: " + describeString + "\n\n\n");
  13.222 +		//		System.out.println("Placemark0");
  13.223 +		//		System.out.println("\n\n\nGot query: " + describeString + "\n\n\n");
  13.224  		logger.info("[Strabon.describe] Executing describe query:" + describeString);
  13.225 -		
  13.226 +
  13.227  		try {
  13.228  			OutputStream out = new FileOutputStream(outFile);
  13.229  			RDFHandler rdfHandler = new NTriplesWriter(out);
  13.230  			graphQuery.evaluate(rdfHandler);
  13.231  			out.close();
  13.232 -			
  13.233 +
  13.234  		} catch (FileNotFoundException e) {
  13.235  			logger.error("[Strabon.describe]", e);
  13.236  		} catch (QueryEvaluationException e) {
  13.237 @@ -955,8 +964,8 @@
  13.238  		}
  13.239  
  13.240  		logger.info("[Strabon.describe] Output: "+outFile);
  13.241 -//		System.out.println("---------------------------------------------");
  13.242 -//		System.out.println("-            DESCRIBE EXECUTED              -");
  13.243 -//		System.out.println("---------------------------------------------");
  13.244 +		//		System.out.println("---------------------------------------------");
  13.245 +		//		System.out.println("-            DESCRIBE EXECUTED              -");
  13.246 +		//		System.out.println("---------------------------------------------");
  13.247  	}
  13.248  }

    14.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
    14.2 +++ b/runtime/src/main/resources/log4j.properties	Tue Jun 19 18:23:47 2012 +0300
    14.3 @@ -0,0 +1,22 @@
    14.4 +# logger level values: OFF, ERROR, WARN, INFO, DEBUG, ALL
    14.5 +log4j.rootLogger=OFF, CA
    14.6 +#log4j.rootLogger=DEBUG, CA
    14.7 +#log4j.rootLogger=INFO, CA, FA
    14.8 +
    14.9 +# Console Appender
   14.10 +log4j.appender.CA=org.apache.log4j.ConsoleAppender
   14.11 +log4j.appender.CA.layout=org.apache.log4j.PatternLayout
   14.12 +log4j.appender.CA.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
   14.13 +
   14.14 +# File Appender
   14.15 +#log4j.appender.FA=org.apache.log4j.FileAppender
   14.16 +#log4j.appender.FA.File=sample.log
   14.17 +#log4j.appender.FA.layout=org.apache.log4j.PatternLayout
   14.18 +#log4j.appender.FA.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
   14.19 +# Set the logger level of File Appender to WARN
   14.20 +#log4j.appender.FA.Threshold = WARN
   14.21 +
   14.22 +
   14.23 +# Sesame configuration (debug only Strabon)
   14.24 +log4j.logger.org.openrdf.query.parser.QueryParserRegistry=INFO
   14.25 +log4j.logger.org.openrdf.sail.generaldb.managers.TripleTableManager=INFO