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From a...@apache.org
Subject [1/3] jena git commit: Deprecate some methods of Capabilities
Date Sun, 01 Jan 2017 13:28:28 GMT
Repository: jena
Updated Branches:
  refs/heads/master 47d216f52 -> 0becdc7e1


Deprecate some methods of Capabilities

addAllowed( everyTriple )
deleteAllowed( everyTriple )
iteratorRemoveAllowed()
canBeEmpty()
findContractSafe()


Project: http://git-wip-us.apache.org/repos/asf/jena/repo
Commit: http://git-wip-us.apache.org/repos/asf/jena/commit/cd19f7bb
Tree: http://git-wip-us.apache.org/repos/asf/jena/tree/cd19f7bb
Diff: http://git-wip-us.apache.org/repos/asf/jena/diff/cd19f7bb

Branch: refs/heads/master
Commit: cd19f7bbba9ddc37205650a0e8a35925572191c2
Parents: ff92139
Author: Andy Seaborne <andy@apache.org>
Authored: Fri Dec 23 22:54:15 2016 +0000
Committer: Andy Seaborne <andy@apache.org>
Committed: Sat Dec 24 17:26:18 2016 +0000

----------------------------------------------------------------------
 .../org/apache/jena/graph/Capabilities.java     |  29 ++-
 .../jena/rdfxml/xmloutput/impl/Abbreviated.java |  13 -
 .../apache/jena/shared/RandomOrderGraph.java    |  16 +-
 .../apache/jena/graph/GraphContractTest.java    | 238 ++++++-------------
 .../jena/graph/test/AbstractTestGraph.java      |  22 +-
 .../jena/graph/test/TestCapabilities.java       |   6 -
 .../jena/rdfxml/xmloutput/PrettyWriterTest.java |  61 -----
 .../reasoner/rulesys/test/TestCapabilities.java |  72 ------
 .../jena/reasoner/rulesys/test/TestPackage.java |   1 -
 .../apache/jena/reasoner/test/TestInfGraph.java |   9 -
 .../permissions/graph/SecuredCapabilities.java  |  13 +-
 .../jena/permissions/impl/SecuredItemImpl.java  |  10 +-
 .../model/SecuredModelDetailTest.java           |  13 +-
 .../src/test/resources/log4j.properties         |   7 +-
 14 files changed, 139 insertions(+), 371 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-core/src/main/java/org/apache/jena/graph/Capabilities.java
----------------------------------------------------------------------
diff --git a/jena-core/src/main/java/org/apache/jena/graph/Capabilities.java b/jena-core/src/main/java/org/apache/jena/graph/Capabilities.java
index d9a52bb..d79d3a1 100644
--- a/jena-core/src/main/java/org/apache/jena/graph/Capabilities.java
+++ b/jena-core/src/main/java/org/apache/jena/graph/Capabilities.java
@@ -18,6 +18,8 @@
 
 package org.apache.jena.graph;
 
+import org.apache.jena.mem.GraphMem;
+
 /**
     Interface for expressing capabilities.
  */
@@ -35,45 +37,56 @@ public interface Capabilities
     boolean addAllowed();
     
     /**
+        Answer true iff Graph::delete() can be used to remove at least some triples
+        from the graph.
+    */
+    boolean deleteAllowed();
+
+    /**
         Answer true if Graph::add() can be used to add at least some triples to the
         graph. If everyTriple is true, answer true iff *any* triple can be added (ie the
         graph places no special restrictions on triples).
+        @deprecated To be removed
     */
+    @Deprecated
     boolean addAllowed( boolean everyTriple );
     
     /**
-        Answer true iff Graph::delete() can be used to remove at least some triples
-        from the graph.
-    */
-    boolean deleteAllowed();
-    
-    /**
         Answer true if Graph::delete() can be used to remove at least some triples 
         from the graph. If everyTriple is true, any such triple may be removed.
+        @deprecated To be removed
     */
+    @Deprecated
     boolean deleteAllowed( boolean everyTriple );
     
     /**
     	Answer true iff the iterators returned from <b>find</b> support the .remove()
         operation. 
+         @deprecated To be removed
     */
+    @Deprecated
     boolean iteratorRemoveAllowed();
     
     /**
         Answer true iff the graph can be completely empty.
+        @deprecated To be removed
      */
+    @Deprecated
     boolean canBeEmpty();
 
     /**
          Answer true if the find() contract on the associated graph is "safe", ie,
          can be used safely by the pretty-printer (we'll tighten up that definition).
+         @deprecated To be removed
      */
+    @Deprecated
     boolean findContractSafe();
 
     /**
         Answer true iff this graph compares literals for equality by value
-        rather than by lexical form (the memory-based graphs do; 
-        TDB model do mostly (because of canonicalization), SDB models don't).
+        in find() operations, rather just applying RDFTerm equality.
+        Only applies to {@link GraphMem}. 
+        TDB models have this effect because of canonicalization for certain datatypes and
ranges, SDB models don't.
     */
     boolean handlesLiteralTyping();
     }

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-core/src/main/java/org/apache/jena/rdfxml/xmloutput/impl/Abbreviated.java
----------------------------------------------------------------------
diff --git a/jena-core/src/main/java/org/apache/jena/rdfxml/xmloutput/impl/Abbreviated.java
b/jena-core/src/main/java/org/apache/jena/rdfxml/xmloutput/impl/Abbreviated.java
index 8a3de2f..a9aec24 100644
--- a/jena-core/src/main/java/org/apache/jena/rdfxml/xmloutput/impl/Abbreviated.java
+++ b/jena-core/src/main/java/org/apache/jena/rdfxml/xmloutput/impl/Abbreviated.java
@@ -19,7 +19,6 @@
 package org.apache.jena.rdfxml.xmloutput.impl;
 
 import java.io.PrintWriter;
-import java.io.Writer;
 
 import org.apache.jena.rdf.model.Model ;
 import org.apache.jena.rdf.model.RDFErrorHandler ;
@@ -114,18 +113,6 @@ public class Abbreviated extends BaseXMLWriter implements RDFErrorHandler
{
 	}
 
 	@Override
-    synchronized public void write(Model baseModel, Writer out, String base)
-	    { 
-		if (baseModel.getGraph().getCapabilities().findContractSafe() == false) 
-            {
-			logger.warn( "Workaround for bugs 803804 and 858163: using RDF/XML (not RDF/XML-ABBREV)
writer  for unsafe graph " + baseModel.getGraph().getClass() );
-			baseModel.write( out, "RDF/XML", base );
-            } 
-        else
-            super.write( baseModel, out, base );
-		}
-		
-	@Override
     protected void writeBody(
 		Model model,
 		PrintWriter pw,

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-core/src/main/java/org/apache/jena/shared/RandomOrderGraph.java
----------------------------------------------------------------------
diff --git a/jena-core/src/main/java/org/apache/jena/shared/RandomOrderGraph.java b/jena-core/src/main/java/org/apache/jena/shared/RandomOrderGraph.java
index 4059b8f..b277916 100644
--- a/jena-core/src/main/java/org/apache/jena/shared/RandomOrderGraph.java
+++ b/jena-core/src/main/java/org/apache/jena/shared/RandomOrderGraph.java
@@ -81,26 +81,30 @@ public class RandomOrderGraph extends WrappedGraph {
 			return parentCapabilities.addAllowed();
 		}
 
-		@Override
+        @Override
+        public boolean deleteAllowed() {
+            return parentCapabilities.deleteAllowed();
+        }
+
+		@SuppressWarnings("deprecation")
+        @Override
         public boolean addAllowed(boolean everyTriple) {
 			return parentCapabilities.addAllowed(everyTriple);
 		}
 
-		@Override
-        public boolean deleteAllowed() {
-			return parentCapabilities.deleteAllowed();
-		}
-
+        @SuppressWarnings("deprecation")
 		@Override
         public boolean deleteAllowed(boolean everyTriple) {
 			return parentCapabilities.deleteAllowed(everyTriple);
 		}
 
+        @SuppressWarnings("deprecation")
 		@Override
         public boolean canBeEmpty() {
 			return parentCapabilities.canBeEmpty();
 		}
 
+        @SuppressWarnings("deprecation")
 		@Override
         public boolean findContractSafe() {
 			return parentCapabilities.findContractSafe();

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-core/src/test/java/org/apache/jena/graph/GraphContractTest.java
----------------------------------------------------------------------
diff --git a/jena-core/src/test/java/org/apache/jena/graph/GraphContractTest.java b/jena-core/src/test/java/org/apache/jena/graph/GraphContractTest.java
index 6f02750..9dfaae8 100644
--- a/jena-core/src/test/java/org/apache/jena/graph/GraphContractTest.java
+++ b/jena-core/src/test/java/org/apache/jena/graph/GraphContractTest.java
@@ -832,25 +832,10 @@ public class GraphContractTest<T extends Graph>  {
 			fail("addAllowed() threw Exception: " + e.toString());
 		}
 		try {
-			c.addAllowed(true);
-		} catch (Exception e) {
-			fail("addAllowed( boolean ) threw Exception: " + e.toString());
-		}
-		try {
 			c.deleteAllowed();
 		} catch (Exception e) {
 			fail("deleteAllowed() threw Exception: " + e.toString());
 		}
-		try {
-			c.deleteAllowed(true);
-		} catch (Exception e) {
-			fail("deleteAllowed( boolean ) threw Exception: " + e.toString());
-		}
-		try {
-			c.canBeEmpty();
-		} catch (Exception e) {
-			fail("canBeEmpty() threw Exception: " + e.toString());
-		}
 	}
 
 	@ContractTest
@@ -1042,9 +1027,6 @@ public class GraphContractTest<T extends Graph>  {
 			assertFalse(g.contains(NodeCreateUtils.createTriple(findCheck)));
 		} catch (UnsupportedOperationException e) {
 			it.close();
-			assertFalse(
-					"delete failed but capailities indicates it should work", g
-							.getCapabilities().iteratorRemoveAllowed());
 		}
 	}
 
@@ -1103,59 +1085,6 @@ public class GraphContractTest<T extends Graph>  {
 		it.close();
 	}
 
-	// public void testStuff()
-	// {
-	// // testAGraph( "StoreMem", new GraphMem() );
-	// // testAGraph( "StoreMemBySubject", new GraphMem() );
-	// // String [] empty = new String [] {};
-	// // Graph g = graphWith( "x R y; p S q; a T b" );
-	// // /* */
-	// // assertContainsAll( "simple graph", g, "x R y; p S q; a T b" );
-	// // graphAdd( g,
-	// "spindizzies lift cities; Diracs communicate instantaneously" );
-	// // g.delete( triple( "x R y" ) );
-	// // g.delete( triple( "a T b" ) );
-	// // assertContainsAll( "modified simple graph", g,
-	// "p S q; spindizzies lift cities; Diracs communicate instantaneously" );
-	// // assertOmitsAll( "modified simple graph", g, "x R y; a T b" );
-	// }
-
-	// /**
-	// Test that Graphs have transaction support methods, and that if they fail
-	// on some g they fail because they do not support the operation.
-	// */
-	// @ContractTest
-	// public void testHasTransactions()
-	// {
-	// Graph g = producer.newInstance();
-	// TransactionHandler th = g.getTransactionHandler();
-	// th.transactionsSupported();
-	// try { th.begin(); } catch (UnsupportedOperationException x) {}
-	// try { th.abort(); } catch (UnsupportedOperationException x) {}
-	// try { th.begin(); th.commit(); } catch (UnsupportedOperationException x)
-	// {}
-	// /* */
-	// Command cmd = new Command()
-	// { @Override
-	// public Object execute() { return null; } };
-	// try { th.executeInTransaction( cmd ); }
-	// catch (UnsupportedOperationException x) {}
-	// }
-	//
-	// @ContractTest
-	// public void testExecuteInTransactionCatchesThrowable()
-	// {Graph g = producer.newInstance();
-	// TransactionHandler th = g.getTransactionHandler();
-	// if (th.transactionsSupported())
-	// {
-	// Command cmd = new Command()
-	// { @Override
-	// public Object execute() throws Error { throw new Error(); } };
-	// try { th.executeInTransaction( cmd ); }
-	// catch (JenaException x) {}
-	// }
-	// }
-
 	@ContractTest
 	public void testAddWithReificationPreamble() {
 		Graph g = producer.newInstance();
@@ -1183,29 +1112,27 @@ public class GraphContractTest<T extends Graph>  {
 
 	@ContractTest
 	public void failingTestDoubleRemoveAll() {
-		final Graph g = producer.newInstance();
-		if (g.getCapabilities().iteratorRemoveAllowed()) {
-			try {
-				graphAddTxn(g, "c S d; e:ff GGG hhhh; _i J 27; Ell Em 'en'");
-				Iterator<Triple> it = new TrackingTripleIterator(
-						g.find(Triple.ANY)) {
-					@Override
-					public void remove() {
-						super.remove(); // removes current
-						g.delete(current); // no-op.
-					}
-				};
-				while (it.hasNext()) {
-					it.next();
-					it.remove();
-				}
-				assertTrue(g.isEmpty());
-			} catch (UnsupportedOperationException e) {
-				fail("Error attempting to remove nodes " + e.getMessage());
-			}
-		}
+	    final Graph g = producer.newInstance();
+	    try {
+	        graphAddTxn(g, "c S d; e:ff GGG hhhh; _i J 27; Ell Em 'en'");
+	        Iterator<Triple> it = new TrackingTripleIterator(g.find(Triple.ANY)) {
+	            @Override
+	            public void remove() {
+	                super.remove(); // removes current
+	                g.delete(current); // no-op.
+	            }
+	        };
+	        while (it.hasNext()) {
+	            it.next();
+	            it.remove();
+	        }
+	        assertTrue(g.isEmpty());
+	    } catch (UnsupportedOperationException e) {
+	        // No Iterator.remove
+	    }
 	}
 
+
 	/**
 	 * Test cases for RemoveSPO(); each entry is a triple (add, remove, result).
 	 * <ul>
@@ -1374,26 +1301,24 @@ public class GraphContractTest<T extends Graph>  {
 	 */
 	@ContractTest
 	public void testIterator_Remove() {
-		Graph graph = graphWith(producer.newInstance(), "a R b; b S e");
-		if (graph.getCapabilities().iteratorRemoveAllowed()) {
-			try {
-				graph.getEventManager().register(GL);
-				txnBegin(graph);
-
-				Triple toRemove = triple("a R b");
-				ExtendedIterator<Triple> rtr = graph.find(toRemove);
-				assertTrue("ensure a(t least) one triple", rtr.hasNext());
-				rtr.next();
-				rtr.remove();
-				rtr.close();
-				GL.assertHas("delete", graph, toRemove);
-			} catch (UnsupportedOperationException e) {
-				fail("Error attempting to remove nodes " + e.getMessage());
-			}
+	    Graph graph = graphWith(producer.newInstance(), "a R b; b S e");
+	    try {
+	        graph.getEventManager().register(GL);
+	        txnBegin(graph);
 
-		}
+	        Triple toRemove = triple("a R b");
+	        ExtendedIterator<Triple> rtr = graph.find(toRemove);
+	        assertTrue("ensure a(t least) one triple", rtr.hasNext());
+	        rtr.next();
+	        rtr.remove();
+	        rtr.close();
+	        GL.assertHas("delete", graph, toRemove);
+	    } catch (UnsupportedOperationException e) {
+	        // No Iterator.remove
+	    }
 	}
 
+
 	@ContractTest
 	public void testTransactionHandler_Commit() {
 		Graph g = producer.newInstance();
@@ -1563,16 +1488,14 @@ public class GraphContractTest<T extends Graph>  {
 
 	@ContractTest
 	public void testSizeAfterRemove() {
-		Graph g = graphWith(producer.newInstance(), "x p y");
-		if (g.getCapabilities().iteratorRemoveAllowed()) {
-			try {
-				ExtendedIterator<Triple> it = g.find(triple("x ?? ??"));
-				it.removeNext();
-				assertEquals(0, g.size());
-			} catch (UnsupportedOperationException e) {
-				fail("Error attempting to remove nodes " + e.getMessage());
-			}
-		}
+	    Graph g = graphWith(producer.newInstance(), "x p y");
+	    try {
+	        ExtendedIterator<Triple> it = g.find(triple("x ?? ??"));
+	        it.removeNext();
+	        assertEquals(0, g.size());
+	    } catch (UnsupportedOperationException e) {
+	        // No Iterator.remove
+	    }
 	}
 
 	@ContractTest
@@ -1664,66 +1587,57 @@ public class GraphContractTest<T extends Graph>  {
 
 	@ContractTest
 	public void testBrokenIndexes() {
-		Graph g = graphWith(producer.newInstance(), "x R y; x S z");
-		if (g.getCapabilities().iteratorRemoveAllowed()) {
-			try {
-				ExtendedIterator<Triple> it = g.find(Node.ANY, Node.ANY,
-						Node.ANY);
-				it.removeNext();
-				it.removeNext();
-				assertFalse(g.find(node("x"), Node.ANY, Node.ANY).hasNext());
-				assertFalse(g.find(Node.ANY, node("R"), Node.ANY).hasNext());
-				assertFalse(g.find(Node.ANY, Node.ANY, node("y")).hasNext());
-			} catch (UnsupportedOperationException e) {
-				fail("Error attempting to remove nodes " + e.getMessage());
-			}
-		}
+	    Graph g = graphWith(producer.newInstance(), "x R y; x S z");
+	    try {
+	        ExtendedIterator<Triple> it = g.find(Node.ANY, Node.ANY,
+	                                             Node.ANY);
+	        it.removeNext();
+	        it.removeNext();
+	        assertFalse(g.find(node("x"), Node.ANY, Node.ANY).hasNext());
+	        assertFalse(g.find(Node.ANY, node("R"), Node.ANY).hasNext());
+	        assertFalse(g.find(Node.ANY, Node.ANY, node("y")).hasNext());
+	    } catch (UnsupportedOperationException e) {
+	        // No Iterator.remove
+	    }
 	}
 
 	@ContractTest
 	public void testBrokenSubject() {
 		Graph g = graphWith(producer.newInstance(), "x brokenSubject y");
-		if (g.getCapabilities().iteratorRemoveAllowed()) {
-			try {
-				ExtendedIterator<Triple> it = g.find(node("x"), Node.ANY,
-						Node.ANY);
-				it.removeNext();
-				assertFalse(g.find(Node.ANY, Node.ANY, Node.ANY).hasNext());
-			} catch (UnsupportedOperationException e) {
-				fail("Error attempting to remove nodes " + e.getMessage());
-			}
+		try {
+		    ExtendedIterator<Triple> it = g.find(node("x"), Node.ANY, Node.ANY);
+		    it.removeNext();
+		    assertFalse(g.find(Node.ANY, Node.ANY, Node.ANY).hasNext());
+		} catch (UnsupportedOperationException e) {
+		    // No Iterator.remove
 		}
 	}
 
 	@ContractTest
 	public void testBrokenPredicate() {
 		Graph g = graphWith(producer.newInstance(), "x brokenPredicate y");
-		if (g.getCapabilities().iteratorRemoveAllowed()) {
-			try {
-				ExtendedIterator<Triple> it = g.find(Node.ANY,
-						node("brokenPredicate"), Node.ANY);
-				it.removeNext();
-				assertFalse(g.find(Node.ANY, Node.ANY, Node.ANY).hasNext());
-			} catch (UnsupportedOperationException e) {
-				fail("Error attempting to remove nodes " + e.getMessage());
-			}
+		try {
+		    ExtendedIterator<Triple> it = g.find(Node.ANY, node("brokenPredicate"), Node.ANY);
+		    it.removeNext();
+		    assertFalse(g.find(Node.ANY, Node.ANY, Node.ANY).hasNext());
+		} catch (UnsupportedOperationException e) {
+		    // No Iterator.remove
 		}
 	}
 
 	@ContractTest
 	public void testBrokenObject() {
-		Graph g = graphWith(producer.newInstance(), "x brokenObject y");
-		if (g.getCapabilities().iteratorRemoveAllowed()) {
-			try {
-				ExtendedIterator<Triple> it = g.find(Node.ANY, Node.ANY,
-						node("y"));
-				it.removeNext();
-				assertFalse(g.find(Node.ANY, Node.ANY, Node.ANY).hasNext());
+	    Graph g = graphWith(producer.newInstance(), "x brokenObject y");
+
+	    try {
+	        ExtendedIterator<Triple> it = g.find(Node.ANY, Node.ANY, node("y"));
+	        it.removeNext();
+	        assertFalse(g.find(Node.ANY, Node.ANY, Node.ANY).hasNext());
+
+	    } catch (UnsupportedOperationException e) {
+	        // No Iterator.remove
+	    }
 
-			} catch (UnsupportedOperationException e) {
-				fail("Error attempting to remove nodes " + e.getMessage());
-			}
-		}
 	}
 
 }

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-core/src/test/java/org/apache/jena/graph/test/AbstractTestGraph.java
----------------------------------------------------------------------
diff --git a/jena-core/src/test/java/org/apache/jena/graph/test/AbstractTestGraph.java b/jena-core/src/test/java/org/apache/jena/graph/test/AbstractTestGraph.java
index 3e3612e..912a257 100644
--- a/jena-core/src/test/java/org/apache/jena/graph/test/AbstractTestGraph.java
+++ b/jena-core/src/test/java/org/apache/jena/graph/test/AbstractTestGraph.java
@@ -388,10 +388,9 @@ public abstract class AbstractTestGraph extends GraphTestBase
             assertFalse( g.contains( NodeCreateUtils.createTriple( findCheck ) ) );
         }
         catch (UnsupportedOperationException e) {
+            // No iterator remove.
             it.close();
-            assertFalse( g.getCapabilities().iteratorRemoveAllowed() ); 
         }
-        it.close();
     }
 
     public void testHasCapabilities()
@@ -400,10 +399,7 @@ public abstract class AbstractTestGraph extends GraphTestBase
         Capabilities c = g.getCapabilities();
         boolean sa = c.sizeAccurate();
         boolean aaSome = c.addAllowed();
-        boolean aaAll = c.addAllowed( true );
         boolean daSome = c.deleteAllowed();
-        boolean daAll = c.deleteAllowed( true );
-        boolean cbe = c.canBeEmpty();
     }
 
     public void testFind()
@@ -522,15 +518,17 @@ public abstract class AbstractTestGraph extends GraphTestBase
     public void testEventDeleteByFind()
     {
         Graph g = getAndRegister( L );
-        if (g.getCapabilities().iteratorRemoveAllowed())
-        {
-            Triple toRemove = triple( "remove this triple" );
-            g.add( toRemove );
+        Triple toRemove = triple( "remove this triple" );
+        g.add( toRemove );
+        try {
             ExtendedIterator<Triple> rtr = g.find( toRemove );
             assertTrue( "ensure a(t least) one triple", rtr.hasNext() );
             rtr.next(); rtr.remove(); rtr.close();
             L.assertHas( new Object[] { "add", g, toRemove, "delete", g, toRemove} );
+        } catch (UnsupportedOperationException ex) {
+            // No iterator remove
         }
+
     }
 
     public void testTwoListeners()
@@ -823,8 +821,8 @@ public abstract class AbstractTestGraph extends GraphTestBase
 
     public void failingTestDoubleRemoveAll() {
         final Graph g = getGraph();
-        if (g.getCapabilities().iteratorRemoveAllowed() ) {
-            graphAdd(g,"c S d; e:ff GGG hhhh; _i J 27; Ell Em 'en'"  );
+        graphAdd(g,"c S d; e:ff GGG hhhh; _i J 27; Ell Em 'en'"  );
+        try {
             Iterator<Triple> it = new TrackingTripleIterator(g.find(Triple.ANY)){
                 @Override
                 public void remove() {
@@ -837,6 +835,8 @@ public abstract class AbstractTestGraph extends GraphTestBase
                 it.remove();
             }
             assertTrue( g.isEmpty() );
+        } catch (UnsupportedOperationException ex) {
+            // Iterator.remove not supported.
         }
     }
 

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-core/src/test/java/org/apache/jena/graph/test/TestCapabilities.java
----------------------------------------------------------------------
diff --git a/jena-core/src/test/java/org/apache/jena/graph/test/TestCapabilities.java b/jena-core/src/test/java/org/apache/jena/graph/test/TestCapabilities.java
index 2e28ba9..4b8de34 100644
--- a/jena-core/src/test/java/org/apache/jena/graph/test/TestCapabilities.java
+++ b/jena-core/src/test/java/org/apache/jena/graph/test/TestCapabilities.java
@@ -90,13 +90,7 @@ public class TestCapabilities extends GraphTestBase
         Capabilities c = new AllFalse();
         boolean b = false;
         b = c.addAllowed();
-        b = c.addAllowed( true );
-        b = c.canBeEmpty();
         b = c.deleteAllowed();
-        b = c.deleteAllowed( false );
         b = c.sizeAccurate();
-        b = c.iteratorRemoveAllowed();
-        b = c.findContractSafe();
-        b = c.handlesLiteralTyping();
         }
     }

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-core/src/test/java/org/apache/jena/rdfxml/xmloutput/PrettyWriterTest.java
----------------------------------------------------------------------
diff --git a/jena-core/src/test/java/org/apache/jena/rdfxml/xmloutput/PrettyWriterTest.java
b/jena-core/src/test/java/org/apache/jena/rdfxml/xmloutput/PrettyWriterTest.java
index 97d890d..cbf194d 100644
--- a/jena-core/src/test/java/org/apache/jena/rdfxml/xmloutput/PrettyWriterTest.java
+++ b/jena-core/src/test/java/org/apache/jena/rdfxml/xmloutput/PrettyWriterTest.java
@@ -20,20 +20,12 @@
 ///////////////
 package org.apache.jena.rdfxml.xmloutput;
 
-// Imports
-///////////////
-
-import java.io.ByteArrayInputStream;
 import java.io.IOException;
-import java.io.OutputStream;
 import java.io.StringReader;
 import java.io.StringWriter;
 import java.util.regex.Pattern;
 
-import org.apache.jena.ontology.OntModel ;
-import org.apache.jena.ontology.OntModelSpec ;
 import org.apache.jena.rdf.model.Model ;
-import org.apache.jena.rdf.model.ModelFactory ;
 import org.apache.jena.rdf.model.test.ModelTestBase ;
 
 public class PrettyWriterTest extends ModelTestBase {
@@ -116,57 +108,4 @@ public class PrettyWriterTest extends ModelTestBase {
 			"file:testing/abbreviated/container.rdf",
 			"<rdf:li.*<rdf:li.*<rdf:li.*<rdf:li");
 	}
-	public void test803804() {
-		String sourceT =
-			"<rdf:RDF "
-				+ " xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'"
-				+ " xmlns:rdfs='http://www.w3.org/2000/01/rdf-schema#'"
-				+ " xmlns:owl=\"http://www.w3.org/2002/07/owl#\">"
-				+ " <owl:ObjectProperty rdf:about="
-				+ "'http://example.org/foo#p'>"
-				+ " </owl:ObjectProperty>"
-				+ "</rdf:RDF>";
-
-		OntModel m =
-			ModelFactory.createOntologyModel(
-				OntModelSpec.OWL_MEM_RULE_INF,
-				null);
-		m.read(
-			new ByteArrayInputStream(sourceT.getBytes()),
-			"http://example.org/foo");
-
-		Model m0 = ModelFactory.createModelForGraph(m.getGraph());
-		/*
-			  Set copyOfm0 = new HashSet();
-			  Set blankNodes = new HashSet();
-			  Iterator it = m0.listStatements();
-			  while (it.hasNext()) {
-			  	Statement st = (Statement)it.next(); 
-				  copyOfm0.add(st);
-				  Resource subj = st.getSubject();
-				  if (subj.isAnon())
-				    blankNodes.add(subj);
-			  }
-			  
-			  it = blankNodes.iterator();
-			  while (it.hasNext()) {
-			  	Resource b = (Resource)it.next();
-			  	Statement st = m0.createStatement(b,OWL.sameAs,b);
-			//  	assertEquals(m0.contains(st),copyOfm0.contains(st));
-			  }
-		*/
-		XMLOutputTestBase.blockLogger();
-		try {
-			m0.write(new OutputStream() {
-				@Override
-                public void write(int b) {
-				}
-			}, "RDF/XML-ABBREV");
-
-		} finally {
-			// This will need to change when the bug is finally fixed.
-			
-			assertTrue(XMLOutputTestBase.unblockLogger());
-		}
-	}
 }

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-core/src/test/java/org/apache/jena/reasoner/rulesys/test/TestCapabilities.java
----------------------------------------------------------------------
diff --git a/jena-core/src/test/java/org/apache/jena/reasoner/rulesys/test/TestCapabilities.java
b/jena-core/src/test/java/org/apache/jena/reasoner/rulesys/test/TestCapabilities.java
deleted file mode 100644
index 0deeab8..0000000
--- a/jena-core/src/test/java/org/apache/jena/reasoner/rulesys/test/TestCapabilities.java
+++ /dev/null
@@ -1,72 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.apache.jena.reasoner.rulesys.test;
-
-import junit.framework.TestCase ;
-import junit.framework.TestSuite ;
-import org.apache.jena.rdf.model.Model ;
-import org.apache.jena.rdf.model.ModelFactory ;
-import org.apache.jena.reasoner.InfGraph ;
-import org.apache.jena.reasoner.Reasoner ;
-import org.apache.jena.reasoner.ReasonerRegistry ;
-
-/**
- * Test harness for checking that graphs generated by the main
- * reasoners report the correct capabilities to things like the RDF writer.
- */
-
-public class TestCapabilities extends TestCase {
-
-    /**
-     * Boilerplate for junit
-     */
-    public TestCapabilities( String name ) {
-        super( name );
-    }
-
-    /**
-     * Boilerplate for junit.
-     * This is its own test suite
-     */
-    public static TestSuite suite() {
-        return new TestSuite( TestCapabilities.class );
-    }
-
-    /**
-     * Test capability returns.
-     */
-    public void testCapabilityValues() {
-        Object[][] testSpec = new Object[][] {
-                {ReasonerRegistry.getOWLMicroReasoner(), Boolean.TRUE},
-                {ReasonerRegistry.getOWLMiniReasoner(), Boolean.TRUE},
-                {ReasonerRegistry.getOWLReasoner(), Boolean.FALSE},
-//                {ReasonerRegistry.getDIGReasoner(), Boolean.FALSE},
-                {ReasonerRegistry.getRDFSReasoner(), Boolean.TRUE},
-                {ReasonerRegistry.getRDFSSimpleReasoner(), Boolean.TRUE},
-        };
-        Model data = ModelFactory.createDefaultModel();
-        for ( Object[] test : testSpec )
-        {
-            Reasoner r = (Reasoner) test[0];
-            Boolean safe = (Boolean) test[1];
-            InfGraph ig = r.bind( data.getGraph() );
-            assertEquals( r.toString(), safe.booleanValue(), ig.getCapabilities().findContractSafe()
);
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-core/src/test/java/org/apache/jena/reasoner/rulesys/test/TestPackage.java
----------------------------------------------------------------------
diff --git a/jena-core/src/test/java/org/apache/jena/reasoner/rulesys/test/TestPackage.java
b/jena-core/src/test/java/org/apache/jena/reasoner/rulesys/test/TestPackage.java
index fe3518c..ad8e26a 100755
--- a/jena-core/src/test/java/org/apache/jena/reasoner/rulesys/test/TestPackage.java
+++ b/jena-core/src/test/java/org/apache/jena/reasoner/rulesys/test/TestPackage.java
@@ -58,7 +58,6 @@ public class TestPackage extends TestSuite {
         addTest( "OWLRuleUnitTests", OWLUnitTest.suite() );
         addTest( "TestBugs", TestBugs.suite() );
         addTest( "TestOWLMisc", TestOWLMisc.suite() );
-        addTest( "TestCapabilities", TestCapabilities.suite() );
         addTest( "TestComparatorBuiltins", TestComparatorBuiltins.suite() );
         addTest( "FRuleEngineIFactoryTest", FRuleEngineIFactoryTest.suite() );
         //addTest ("TestRuleLoader", TestRuleLoader.suite() );

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-core/src/test/java/org/apache/jena/reasoner/test/TestInfGraph.java
----------------------------------------------------------------------
diff --git a/jena-core/src/test/java/org/apache/jena/reasoner/test/TestInfGraph.java b/jena-core/src/test/java/org/apache/jena/reasoner/test/TestInfGraph.java
index 22eca40..7641331 100644
--- a/jena-core/src/test/java/org/apache/jena/reasoner/test/TestInfGraph.java
+++ b/jena-core/src/test/java/org/apache/jena/reasoner/test/TestInfGraph.java
@@ -52,13 +52,4 @@ public class TestInfGraph extends AbstractTestGraph
         InfGraph ig = getInfGraph();
         assertSame( ig.getPrefixMapping(), ig.getRawGraph().getPrefixMapping() );
         }
-    
-    /**
-         Placeholder. Will need revision later.
-    */
-    public void testInfCapabilities()
-        {
-        // The default Ontology inference model is RDFS which is safe
-        assertTrue( getInfGraph().getCapabilities().findContractSafe() );
-        }
     }

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-permissions/src/main/java/org/apache/jena/permissions/graph/SecuredCapabilities.java
----------------------------------------------------------------------
diff --git a/jena-permissions/src/main/java/org/apache/jena/permissions/graph/SecuredCapabilities.java
b/jena-permissions/src/main/java/org/apache/jena/permissions/graph/SecuredCapabilities.java
index 67cf047..d9ca28f 100644
--- a/jena-permissions/src/main/java/org/apache/jena/permissions/graph/SecuredCapabilities.java
+++ b/jena-permissions/src/main/java/org/apache/jena/permissions/graph/SecuredCapabilities.java
@@ -69,7 +69,8 @@ public class SecuredCapabilities implements Capabilities
 	 * @sec.graph Update
 	 * @sec.triple Create (if everyTriple is true)
 	 */
-	@Override
+	@SuppressWarnings("deprecation")
+    @Override
 	public boolean addAllowed( final boolean everyTriple )
 	{
 		Object principal = securityEvaluator.getPrincipal();
@@ -85,7 +86,8 @@ public class SecuredCapabilities implements Capabilities
 		return retval;
 	}
 
-	@Override
+	@SuppressWarnings("deprecation")
+    @Override
 	public boolean canBeEmpty()
 	{
 		return capabilities.canBeEmpty();
@@ -105,6 +107,7 @@ public class SecuredCapabilities implements Capabilities
 	 * @sec.graph Update
 	 * @sec.triple Delete (if everyTriple is true)
 	 */
+	@SuppressWarnings("deprecation")
 	@Override
 	public boolean deleteAllowed( final boolean everyTriple )
 	{
@@ -121,7 +124,8 @@ public class SecuredCapabilities implements Capabilities
 		return retval;
 	}
 
-	@Override
+	@SuppressWarnings("deprecation")
+    @Override
 	public boolean findContractSafe()
 	{
 		return capabilities.findContractSafe();
@@ -136,7 +140,8 @@ public class SecuredCapabilities implements Capabilities
 	/**
 	 * @sec.graph Update
 	 */
-	@Override
+	@SuppressWarnings("deprecation")
+    @Override
 	public boolean iteratorRemoveAllowed()
 	{
 		return securityEvaluator.evaluate(securityEvaluator.getPrincipal(), Action.Update, graphIRI)

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-permissions/src/main/java/org/apache/jena/permissions/impl/SecuredItemImpl.java
----------------------------------------------------------------------
diff --git a/jena-permissions/src/main/java/org/apache/jena/permissions/impl/SecuredItemImpl.java
b/jena-permissions/src/main/java/org/apache/jena/permissions/impl/SecuredItemImpl.java
index 182d30e..fd9a03e 100644
--- a/jena-permissions/src/main/java/org/apache/jena/permissions/impl/SecuredItemImpl.java
+++ b/jena-permissions/src/main/java/org/apache/jena/permissions/impl/SecuredItemImpl.java
@@ -52,7 +52,7 @@ public abstract class SecuredItemImpl implements SecuredItem {
 	// a key for the secured item.
 	private class CacheKey implements Comparable<CacheKey> {
 		private final Action action;
-        private final Node modelNode;
+        private final Node mNode;
 		private final Triple from;
 		private final Triple to;
 		private Integer hashCode;
@@ -69,7 +69,7 @@ public abstract class SecuredItemImpl implements SecuredItem {
 		public CacheKey(final Action action, final Node modelNode,
 				final Triple to, final Triple from) {
 			this.action = action;
-			this.modelNode = modelNode;
+			this.mNode = modelNode;
 			this.to = to;
 			this.from = from;
 		}
@@ -111,8 +111,8 @@ public abstract class SecuredItemImpl implements SecuredItem {
 		public int compareTo(final CacheKey other) {
 			int retval = this.action.compareTo(other.action);
 			if (retval == Expr.CMP_EQUAL) {
-				retval = NodeUtils.compareRDFTerms(this.modelNode,
-						other.modelNode);
+				retval = NodeUtils.compareRDFTerms(this.mNode,
+						other.mNode);
 			}
 			if (retval == Expr.CMP_EQUAL) {
 				retval = compare(this.to, other.to);
@@ -135,7 +135,7 @@ public abstract class SecuredItemImpl implements SecuredItem {
 		public int hashCode() {
 			if (hashCode == null) {
 				hashCode = new HashCodeBuilder().append(action)
-						.append(modelNode).append(from).append(to).toHashCode();
+						.append(mNode).append(from).append(to).toHashCode();
 			}
 			return hashCode;
 		}

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-permissions/src/test/java/org/apache/jena/permissions/model/SecuredModelDetailTest.java
----------------------------------------------------------------------
diff --git a/jena-permissions/src/test/java/org/apache/jena/permissions/model/SecuredModelDetailTest.java
b/jena-permissions/src/test/java/org/apache/jena/permissions/model/SecuredModelDetailTest.java
index eef28b9..5840969 100644
--- a/jena-permissions/src/test/java/org/apache/jena/permissions/model/SecuredModelDetailTest.java
+++ b/jena-permissions/src/test/java/org/apache/jena/permissions/model/SecuredModelDetailTest.java
@@ -43,10 +43,8 @@ public class SecuredModelDetailTest {
 	private Model baseModel;
 	private SecuredModel securedModel;
 	private DetailEvaluator secEval;
-	private Property pTo = ResourceFactory
-			.createProperty("http://example.com/to");
-	private Property pFrom = ResourceFactory
-			.createProperty("http://example.com/from");
+	private static Property pTo = ResourceFactory.createProperty("http://example.com/to");
+	private static Property pFrom = ResourceFactory.createProperty("http://example.com/from");
 
 	@Before
 	public void setup() {
@@ -273,12 +271,7 @@ public class SecuredModelDetailTest {
 
 		private Principal principal;
 		private Model model;
-		private RDFNode msgType = ResourceFactory
-				.createResource("http://example.com/msg");
-        private Property pTo = ResourceFactory
-				.createProperty("http://example.com/to");
-        private Property pFrom = ResourceFactory
-				.createProperty("http://example.com/from");
+		private RDFNode msgType = ResourceFactory.createResource("http://example.com/msg");
 
 		/**
 		 * 

http://git-wip-us.apache.org/repos/asf/jena/blob/cd19f7bb/jena-permissions/src/test/resources/log4j.properties
----------------------------------------------------------------------
diff --git a/jena-permissions/src/test/resources/log4j.properties b/jena-permissions/src/test/resources/log4j.properties
index f3d6f5e..84ecb9f 100644
--- a/jena-permissions/src/test/resources/log4j.properties
+++ b/jena-permissions/src/test/resources/log4j.properties
@@ -1,3 +1,4 @@
+# Testing
 log4j.rootLogger=INFO, stdlog
 
 log4j.appender.stdlog=org.apache.log4j.ConsoleAppender
@@ -10,6 +11,6 @@ log4j.logger.org.apache.jena.arq.info=INFO
 log4j.logger.org.apache.jena.arq.exec=INFO
 
 # Everything else in Jena
-log4j.logger.org.apache.jena=WARN
-log4j.logger.org.apache.jena=WARN
-log4j.logger.org.apache.jena.riot=INFO
+# Off for permissions testing
+log4j.logger.org.apache.jena=ERROR
+log4j.logger.org.apache.jena.riot=ERROR


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