[Bigdata-commit] SF.net SVN: bigdata:[8038] branches/RDR/bigdata-sails/src/test/com/bigdata/ rdf/sail

[<mrp...@us...>]

Revision: 8038
          http://sourceforge.net/p/bigdata/code/8038
Author:   mrpersonick
Date:     2014-04-03 21:32:58 +0000 (Thu, 03 Apr 2014)
Log Message:
-----------
added an analytic to produce a connected subgraph between a source and one or more targets

Added Paths:
-----------
    branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/
    branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/TestPaths.java
    branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths1.rq
    branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths1.ttl
    branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths2.rq
    branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths2.ttl
    branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths3.rq
    branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths3.ttl
    branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths4.rq
    branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths4.ttl

Added: branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/TestPaths.java
===================================================================
--- branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/TestPaths.java	                        (rev 0)
+++ branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/TestPaths.java	2014-04-03 21:32:58 UTC (rev 8038)
@@ -0,0 +1,220 @@
+/**
+Copyright (C) SYSTAP, LLC 2006-2007.  All rights reserved.
+
+Contact:
+     SYSTAP, LLC
+     4501 Tower Road
+     Greensboro, NC 27410
+     lic...@bi...
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; version 2 of the License.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+*/
+/*
+ * Created on Sep 16, 2009
+ */
+
+package com.bigdata.rdf.sail.graph;
+
+import java.io.InputStream;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+import org.openrdf.model.URI;
+import org.openrdf.model.impl.URIImpl;
+import org.openrdf.query.QueryLanguage;
+import org.openrdf.query.TupleQuery;
+import org.openrdf.query.TupleQueryResult;
+import org.openrdf.rio.RDFFormat;
+
+import com.bigdata.rdf.axioms.NoAxioms;
+import com.bigdata.rdf.sail.BigdataSail;
+import com.bigdata.rdf.sail.BigdataSailRepository;
+import com.bigdata.rdf.sail.BigdataSailRepositoryConnection;
+import com.bigdata.rdf.sail.ProxyBigdataSailTestCase;
+import com.bigdata.rdf.vocab.BaseVocabulary;
+import com.bigdata.rdf.vocab.NoVocabulary;
+import com.bigdata.rdf.vocab.RDFSVocabulary;
+import com.bigdata.rdf.vocab.VocabularyDecl;
+
+public class TestPaths extends ProxyBigdataSailTestCase {
+
+    protected static final Logger log = Logger.getLogger(TestPaths.class);
+
+    protected static final boolean INFO = log.isInfoEnabled();
+    
+    @Override
+    public Properties getProperties() {
+        
+        Properties props = super.getProperties();
+
+        props.setProperty(BigdataSail.Options.AXIOMS_CLASS, NoAxioms.class.getName());
+        props.setProperty(BigdataSail.Options.VOCABULARY_CLASS, NoVocabulary.class.getName());
+        props.setProperty(BigdataSail.Options.TRUTH_MAINTENANCE, "false");
+        props.setProperty(BigdataSail.Options.JUSTIFY, "false");
+        props.setProperty(BigdataSail.Options.TEXT_INDEX, "false");
+        
+        return props;
+        
+    }
+    
+    /**
+     * 
+     */
+    public TestPaths() {
+    }
+
+    /**
+     * @param arg0
+     */
+    public TestPaths(String arg0) {
+        super(arg0);
+    }
+    
+    protected void load(final BigdataSailRepositoryConnection cxn, final String resource) throws Exception {
+    	
+    	final InputStream is = getClass().getResourceAsStream(resource);
+    	
+    	cxn.add(is, "", RDFFormat.TURTLE);
+    	
+    }
+    
+    protected InputStream open(final String resource) throws Exception {
+    	
+    	return getClass().getResourceAsStream(resource);
+    	
+    }
+    
+//    public void testSimpleBFS() throws Exception {
+//    	
+//    	final BigdataSail sail = getSail();
+//    	sail.initialize();
+//    	final BigdataSailRepository repo = new BigdataSailRepository(sail);
+//    	
+//    	final BigdataSailRepositoryConnection cxn = repo.getConnection();
+//        cxn.setAutoCommit(false);
+//        
+//        try {
+//    
+//        	cxn.add(open("paths1.ttl"), "", RDFFormat.TURTLE);
+//        	cxn.commit();
+//        	
+//        	log.trace("\n"+sail.getDatabase().dumpStore());
+//        	
+//        	final String query = IOUtils.toString(open("paths1.rq"));
+//        	
+//        	log.trace("\n"+query);
+//        	
+//        	final TupleQuery tqr = cxn.prepareTupleQuery(QueryLanguage.SPARQL, query);
+//        	
+//        	final TupleQueryResult result = tqr.evaluate();
+//        	
+//        	while (result.hasNext()) {
+//        		
+//        		log.trace(result.next());
+//        		
+//        	}
+//        	
+//        	result.close();
+//            
+//        } finally {
+//            cxn.close();
+//            sail.__tearDownUnitTest();
+//        }
+//
+//    }
+//
+//    public void testSimpleSSSP() throws Exception {
+//    	
+//    	final BigdataSail sail = getSail();
+//    	sail.initialize();
+//    	final BigdataSailRepository repo = new BigdataSailRepository(sail);
+//    	
+//    	final BigdataSailRepositoryConnection cxn = repo.getConnection();
+//        cxn.setAutoCommit(false);
+//        
+//        try {
+//    
+//        	cxn.add(open("paths2.ttl"), "", RDFFormat.TURTLE);
+//        	cxn.commit();
+//        	
+//        	log.trace("\n"+sail.getDatabase().dumpStore());
+//        	
+//        	final String query = IOUtils.toString(open("paths2.rq"));
+//        	
+//        	log.trace("\n"+query);
+//        	
+//        	final TupleQuery tqr = cxn.prepareTupleQuery(QueryLanguage.SPARQL, query);
+//        	
+//        	final TupleQueryResult result = tqr.evaluate();
+//        	
+//        	while (result.hasNext()) {
+//        		
+//        		log.trace(result.next());
+//        		
+//        	}
+//        	
+//        	result.close();
+//            
+//        } finally {
+//            cxn.close();
+//            sail.__tearDownUnitTest();
+//        }
+//
+//    }
+
+    public void testPaths() throws Exception {
+    	
+    	final BigdataSail sail = getSail();
+    	sail.initialize();
+    	final BigdataSailRepository repo = new BigdataSailRepository(sail);
+    	
+    	final BigdataSailRepositoryConnection cxn = repo.getConnection();
+        cxn.setAutoCommit(false);
+        
+        try {
+    
+        	cxn.add(open("paths4.ttl"), "", RDFFormat.TURTLE);
+        	cxn.commit();
+        	
+        	log.trace("\n"+sail.getDatabase().dumpStore());
+        	
+        	final String query = IOUtils.toString(open("paths4.rq"));
+        	
+        	log.trace("\n"+query);
+        	
+        	final TupleQuery tqr = cxn.prepareTupleQuery(QueryLanguage.SPARQL, query);
+        	
+        	final TupleQueryResult result = tqr.evaluate();
+        	
+        	while (result.hasNext()) {
+        		
+        		log.trace(result.next());
+        		
+        	}
+        	
+        	result.close();
+            
+        } finally {
+            cxn.close();
+            sail.__tearDownUnitTest();
+        }
+
+    }
+
+}


Property changes on: branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/TestPaths.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths1.rq
===================================================================
--- branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths1.rq	                        (rev 0)
+++ branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths1.rq	2014-04-03 21:32:58 UTC (rev 8038)
@@ -0,0 +1,11 @@
+PREFIX gas: <http://www.bigdata.com/rdf/gas#>
+SELECT * {
+  SERVICE gas:service {
+    gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
+    gas:program gas:in </:source> . # starting point
+    gas:program gas:target </:target> . # target vertices
+    gas:program gas:out ?v . # bound to the visited vertices.
+    gas:program gas:out1 ?depth . # bound to the depth of the visited vertices.
+    gas:program gas:out2 ?pred . # bound to the predecessor.
+  }
+} order by ?depth
\ No newline at end of file

Added: branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths1.ttl
===================================================================
--- branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths1.ttl	                        (rev 0)
+++ branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths1.ttl	2014-04-03 21:32:58 UTC (rev 8038)
@@ -0,0 +1,13 @@
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix bd: <http://www.bigdata.com/rdf#> .
+@prefix : <:> .
+
+# first path
+:source :edge :a .
+:a :edge :b .
+:b :edge :target .
+
+# second path
+:source :edge :c .
+:c :edge :d .
+:d :edge :target .

Added: branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths2.rq
===================================================================
--- branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths2.rq	                        (rev 0)
+++ branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths2.rq	2014-04-03 21:32:58 UTC (rev 8038)
@@ -0,0 +1,11 @@
+PREFIX gas: <http://www.bigdata.com/rdf/gas#>
+SELECT * {
+  SERVICE gas:service {
+    gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.SSSP" .
+    gas:program gas:in </:source> . # starting point
+    gas:program gas:target </:target> . # target vertices
+    gas:program gas:out ?s . # bound to the visited vertices.
+    gas:program gas:out1 ?distance . # bound to the distance of the visited vertices.
+    gas:program gas:out2 ?pred . # bound to the predecessor
+  }
+} order by ?distance
\ No newline at end of file

Added: branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths2.ttl
===================================================================
--- branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths2.ttl	                        (rev 0)
+++ branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths2.ttl	2014-04-03 21:32:58 UTC (rev 8038)
@@ -0,0 +1,22 @@
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix bd: <http://www.bigdata.com/rdf#> .
+@prefix : <:> .
+
+# first path, length = 2
+:source :edge :a .
+:a :edge :b .
+:b :edge :target .
+
+# second path, length = 2
+:source :edge :c .
+:c :edge :d .
+:d :edge :target .
+
+# third path, length = 3
+:source :edge :e .
+:e :edge :f .
+:f :edge :g .
+:g :edge :target .
+
+# extraneous
+:target :edge :extraneous .

Added: branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths3.rq
===================================================================
--- branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths3.rq	                        (rev 0)
+++ branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths3.rq	2014-04-03 21:32:58 UTC (rev 8038)
@@ -0,0 +1,16 @@
+PREFIX gas: <http://www.bigdata.com/rdf/gas#>
+SELECT * {
+  SERVICE gas:service {
+    gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.PATHS" .
+    gas:program gas:in </:target> . # starting point
+    gas:program gas:target </:source> . # target vertices
+    gas:program gas:traversalDirection "Reverse" .
+    gas:program gas:maxIterationsAfterTargets 2 .
+    # set this to something that reasonably constrains the runtime
+    gas:program gas:maxVisited 100000 . 
+    gas:program gas:out ?s . # bound to the visited vertices.
+    gas:program gas:out1 ?depth . # bound to the depth
+  }
+  #?s </:edge> ?o .
+  #filter(!sameTerm(?s,</:target>)) .
+} order by ?depth
\ No newline at end of file

Added: branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths3.ttl
===================================================================
--- branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths3.ttl	                        (rev 0)
+++ branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths3.ttl	2014-04-03 21:32:58 UTC (rev 8038)
@@ -0,0 +1,33 @@
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix bd: <http://www.bigdata.com/rdf#> .
+@prefix : <:> .
+
+# first path, length = 2
+:source :edge :a .
+:a :edge :b .
+:b :edge :target .
+
+# second path, length = 2
+:source :edge :c .
+:c :edge :d .
+:d :edge :target .
+
+# third path, length = 3
+:source :edge :e .
+:e :edge :f .
+:f :edge :g .
+:g :edge :target .
+
+# third path, length = 4
+:source :edge :h .
+:h :edge :i .
+:i :edge :j .
+:j :edge :k .
+:k :edge :target .
+
+# extraneous
+:target :edge :extraneous .
+
+# cycle
+:b :edge :cycle .
+:cycle :edge :a .

Added: branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths4.rq
===================================================================
--- branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths4.rq	                        (rev 0)
+++ branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths4.rq	2014-04-03 21:32:58 UTC (rev 8038)
@@ -0,0 +1,18 @@
+PREFIX gas: <http://www.bigdata.com/rdf/gas#>
+SELECT * {
+  SERVICE gas:service {
+    gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.PATHS" .
+    gas:program gas:in </:target> . # starting point
+    gas:program gas:target </:source1> . # target vertices
+    gas:program gas:target </:source2> . # target vertices
+    gas:program gas:traversalDirection "Reverse" .
+    # gas:program gas:maxIterations 2 .
+    gas:program gas:maxIterationsAfterTargets 0 .
+    # set this to something that reasonably constrains the runtime
+    gas:program gas:maxVisited 100000 . 
+    gas:program gas:out ?s . # bound to the visited vertices.
+    gas:program gas:out1 ?depth . # bound to the depth
+  }
+  ?s </:edge> ?o .
+  filter(?s != </:target>) .
+} order by ?depth
\ No newline at end of file

Added: branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths4.ttl
===================================================================
--- branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths4.ttl	                        (rev 0)
+++ branches/RDR/bigdata-sails/src/test/com/bigdata/rdf/sail/graph/paths4.ttl	2014-04-03 21:32:58 UTC (rev 8038)
@@ -0,0 +1,36 @@
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix bd: <http://www.bigdata.com/rdf#> .
+@prefix : <:> .
+
+# first path from source1, length = 2
+:source1 :edge :b .
+:b :edge :a .
+:a :edge :target .
+
+# second path from source1, length = 3
+:source1 :edge :e .
+:e :edge :d .
+:d :edge :c .
+:c :edge :target .
+
+# first path from source2, length = 3
+:source2 :edge :h .
+:h :edge :g .
+:g :edge :f .
+:f :edge :target .
+
+# second path from source2, length = 4
+:source2 :edge :l .
+:l :edge :k .
+:k :edge :j .
+:j :edge :i .
+:i :edge :target .
+
+# only path from source3, length = 5
+:source3 :edge :z .
+:z :edge :y .
+:y :edge :x .
+:x :edge :w .
+:w :edge :v .
+:v :edge :target .
+

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