Author: jm
Date: 2011-09-20 11:00:53 -0700 (Tue, 20 Sep 2011)
New Revision: 26881
Added:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkTableManager.java
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNetworkTableManagerTest.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkTableManagerImpl.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkTableManagerTest.java
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableManager.java
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableMetadata.java
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyTableManagerTest.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableManagerImpl.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableMetadataImpl.java
core3/impl/trunk/model-impl/impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/impl/trunk/model-impl/impl/src/main/resources/META-INF/spring/bundle-context.xml
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/NetworkTestSupport.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/subnetwork/CySubNetworkCyTableManagerTest.java
Log:
Ooops, forgot to commit changes to model-api and model-impl
Added:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkTableManager.java
===================================================================
---
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkTableManager.java
(rev 0)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkTableManager.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -0,0 +1,36 @@
+package org.cytoscape.model;
+
+import java.util.Map;
+
+/**
+ * Provides access to all network-table relationships.
+ */
+public interface CyNetworkTableManager {
+ /**
+ * Associates the given table to the network using the specified
namespace and type.
+ */
+ void setTable(CyNetwork network, Class<? extends CyTableEntry> type,
String namespace, CyTable table);
+
+ /**
+ * Returns the table with the specified namespace and type from the
+ * network.
+ */
+ CyTable getTable(CyNetwork network, Class<? extends CyTableEntry> type,
String namespace);
+
+ /**
+ * Removes the table with the specified namespace and type from
+ * the network.
+ */
+ void removeTable(CyNetwork network, Class<? extends CyTableEntry> type,
String namespace);
+
+ /**
+ * Returns a read-only map of all of the tables for the specified type
+ * from the network. Each table is keyed by its namespace.
+ */
+ Map<String, CyTable> getTables(CyNetwork network, Class<? extends
CyTableEntry> type);
+
+ /**
+ * Clears all the network-table relationships.
+ */
+ void reset();
+}
Property changes on:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkTableManager.java
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableManager.java
===================================================================
---
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableManager.java
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableManager.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -28,7 +28,6 @@
package org.cytoscape.model;
-import java.util.Map;
import java.util.Set;
@@ -38,18 +37,6 @@
*/
public interface CyTableManager {
/**
- * Returns a map of table names to tables, which contain the attributes
- * for the specified network.
- *
- * @param type The type of map to retrieve: CyNode, CyEdge, or
CyNetwork (for now).
- * @param network The network associated with the map.
- *
- * @return a map of table names to tables, which contain the attributes
- * for the specified network.
- */
- public Map<String, CyTable> getTableMap(Class<?> type, CyNetwork
network);
-
- /**
* Returns a Set of all tables with the specified visibility.
* @param includePrivate Whether to include private CyTables
* in the list (i.e. all possible CyTables) or not.
@@ -57,7 +44,7 @@
* including private CyTables (i.e. meaning all possible
* CyTables) or just public CyTables.
*/
- Set<CyTableMetadata> getAllTables(boolean includePrivate);
+ Set<CyTable> getAllTables(boolean includePrivate);
/** Registers a new table with the manager and fires a TableAddedEvent
event.
* @param table a non-null CyTable that will be added to the manager
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableMetadata.java
===================================================================
---
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableMetadata.java
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableMetadata.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -1,10 +1,8 @@
package org.cytoscape.model;
-import java.util.Set;
-
/**
- * A snapshot of information about the relationships shared between a CyTable
- * instance and any associated CyNetworks.
+ * A snapshot of information about a relationship shared between a CyTable
+ * instance and an associated CyNetworks.
*/
public interface CyTableMetadata {
/**
@@ -25,7 +23,7 @@
* Returns all the networks associated with this object's table.
* @return all the networks associated with this object's table.
*/
- Set<CyNetwork> getCyNetworks();
+ CyNetwork getCyNetwork();
/**
* Returns the namespace used as the key to this object's table in
Added:
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNetworkTableManagerTest.java
===================================================================
---
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNetworkTableManagerTest.java
(rev 0)
+++
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNetworkTableManagerTest.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -0,0 +1,135 @@
+package org.cytoscape.model;
+
+import static org.junit.Assert.*;
+import static org.mockito.Mockito.mock;
+
+import java.util.Map;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public abstract class AbstractCyNetworkTableManagerTest {
+ /**
+ * Must be supplied by implementer.
+ */
+ protected CyNetworkTableManager mgr;
+
+ /**
+ * Must be supplied by implementer.
+ */
+ protected CyNetwork goodNetwork;
+
+ private CyNetwork badNetwork;
+ private CyTable table1;
+ private CyTable table2;
+
+ @Before
+ public void setUp() {
+ badNetwork = mock(CyNetwork.class);
+ table1 = mock(CyTable.class);
+ table2 = mock(CyTable.class);
+ }
+
+ @Test
+ public void testGoodNetwork() {
+ assertNotNull( mgr.getTables(goodNetwork, CyNetwork.class) );
+ assertNotNull( mgr.getTables(goodNetwork, CyNode.class) );
+ assertNotNull( mgr.getTables(goodNetwork, CyEdge.class) );
+ }
+
+ @Test
+ public void testBadNetwork() {
+ assertEquals( 0, mgr.getTables(badNetwork,
CyNetwork.class).size() );
+ assertEquals( 0, mgr.getTables(badNetwork, CyNode.class).size()
);
+ assertEquals( 0, mgr.getTables(badNetwork, CyEdge.class).size()
);
+ }
+
+ @Test
+ public void testNullNetwork() {
+ try {
+ mgr.getTables(null, CyNetwork.class);
+ fail();
+ } catch (IllegalArgumentException e) {
+ }
+ try {
+ mgr.getTables(null, CyNode.class);
+ fail();
+ } catch (IllegalArgumentException e) {
+ }
+ try {
+ mgr.getTables(null, CyEdge.class);
+ fail();
+ } catch (IllegalArgumentException e) {
+ }
+ }
+
+ @Test
+ public void testTableNetworkMapHasExpectedTables() throws Exception {
+ checkTableMap( mgr.getTables(goodNetwork, CyNetwork.class) );
+ checkTableMap( mgr.getTables(goodNetwork, CyNode.class) );
+ checkTableMap( mgr.getTables(goodNetwork, CyEdge.class) );
+ }
+
+ private void checkTableMap(Map<String,CyTable> tableMap) {
+ // we should have at least the two default, but others may exist
+ assertTrue(tableMap.size() >= 2);
+ assertTrue(tableMap.keySet().contains(CyNetwork.DEFAULT_ATTRS));
+ assertTrue(tableMap.keySet().contains(CyNetwork.HIDDEN_ATTRS));
+ }
+
+ @Test
+ public void testSetTable() throws Exception {
+ String namespace = "foo";
+ mgr.setTable(goodNetwork, CyNode.class, namespace, table1);
+ CyTable other = mgr.getTable(goodNetwork, CyNode.class,
namespace);
+ assertSame(table1, other);
+ }
+
+ @Test
+ public void testOverwriteTable() throws Exception {
+ String namespace = "foo";
+ mgr.setTable(goodNetwork, CyNode.class, namespace, table1);
+ mgr.setTable(goodNetwork, CyNode.class, namespace, table2);
+ CyTable other = mgr.getTable(goodNetwork, CyNode.class,
namespace);
+ assertSame(table2, other);
+ }
+
+ @Test
+ public void testRemoveTable() throws Exception {
+ String namespace = "foo";
+ mgr.setTable(goodNetwork, CyNode.class, namespace, table1);
+ mgr.removeTable(goodNetwork, CyNode.class, namespace);
+ CyTable other = mgr.getTable(goodNetwork, CyNode.class,
namespace);
+ assertNull(other);
+ }
+
+ @Test
+ public void testGetTables() throws Exception {
+ String namespace = "foo";
+ mgr.setTable(goodNetwork, CyNode.class, namespace, table1);
+ Map<String, CyTable> tables = mgr.getTables(goodNetwork,
CyNode.class);
+ assertSame(table1, tables.get(namespace));
+ }
+
+ @Test
+ public void testRemoveDefaultTables() throws Exception {
+ for (Class<? extends CyTableEntry> type : new Class[] {
CyNetwork.class, CyNode.class, CyEdge.class }) {
+ try {
+ mgr.removeTable(goodNetwork, type,
CyNetwork.DEFAULT_ATTRS);
+ fail();
+ } catch (IllegalArgumentException e) {
+ }
+ }
+ }
+
+ @Test
+ public void testSetDefaultTables() throws Exception {
+ for (Class<? extends CyTableEntry> type : new Class[] {
CyNetwork.class, CyNode.class, CyEdge.class }) {
+ try {
+ mgr.setTable(goodNetwork, type,
CyNetwork.DEFAULT_ATTRS, table1);
+ fail();
+ } catch (IllegalArgumentException e) {
+ }
+ }
+ }
+}
Property changes on:
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNetworkTableManagerTest.java
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Modified:
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyTableManagerTest.java
===================================================================
---
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyTableManagerTest.java
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyTableManagerTest.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -28,15 +28,14 @@
package org.cytoscape.model;
-import static org.mockito.Mockito.mock;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.*;
import org.junit.Before;
import org.junit.Test;
-import java.util.Map;
-
public abstract class AbstractCyTableManagerTest {
/**
* Must be supplied by implementer.
@@ -48,48 +47,11 @@
*/
protected CyNetwork goodNetwork;
- private CyNetwork badNetwork;
-
@Before
public void setUp() {
- badNetwork = mock(CyNetwork.class);
}
@Test
- public void testGoodNetwork() {
- assertNotNull( mgr.getTableMap(CyNetwork.class, goodNetwork) );
- assertNotNull( mgr.getTableMap(CyNode.class, goodNetwork) );
- assertNotNull( mgr.getTableMap(CyEdge.class, goodNetwork) );
- }
-
- @Test
- public void testBadNetwork() {
- assertNull( mgr.getTableMap(CyNetwork.class,badNetwork) );
- assertNull( mgr.getTableMap(CyNode.class,badNetwork) );
- assertNull( mgr.getTableMap(CyEdge.class,badNetwork) );
- }
-
- @Test
- public void testNullNetwork() {
- assertNull( mgr.getTableMap(CyNetwork.class,null) );
- assertNull( mgr.getTableMap(CyNode.class,null) );
- assertNull( mgr.getTableMap(CyEdge.class,null) );
- }
-
- public void testTableNetworkMapHasExpectedTables() throws Exception {
- checkTableMap( mgr.getTableMap(CyNetwork.class, goodNetwork) );
- checkTableMap( mgr.getTableMap(CyNode.class, goodNetwork) );
- checkTableMap( mgr.getTableMap(CyEdge.class, goodNetwork) );
- }
-
- private void checkTableMap(Map<String,CyTable> tableMap) {
- // we should have at least the two default, but others may exist
- assertTrue(tableMap.size() >= 2);
- assertTrue(tableMap.keySet().contains(CyNetwork.DEFAULT_ATTRS));
- assertTrue(tableMap.keySet().contains(CyNetwork.HIDDEN_ATTRS));
- }
-
- @Test
public void testReset() {
mgr.addTable(goodNetwork.getDefaultNodeTable());
assertFalse(mgr.getAllTables(true).isEmpty());
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -88,6 +88,7 @@
private final List<CySubNetwork> subNetworks;
private final CySubNetwork base;
private final CyTableManagerImpl tableMgr;
+ private final CyNetworkTableManagerImpl networkTableMgr;
private final CyTableFactory tableFactory;
private final CyServiceRegistrar serviceRegistrar;
@@ -98,10 +99,12 @@
* @param eh The CyEventHelper used for firing events.
*/
public ArrayGraph(final CyEventHelper eh, final CyTableManagerImpl
tableMgr,
- final CyTableFactory tableFactory,
+ final CyNetworkTableManagerImpl
networkTableMgr,
+ final CyTableFactory tableFactory,
final CyServiceRegistrar serviceRegistrar, final
boolean publicTables)
{
this.tableMgr = tableMgr;
+ this.networkTableMgr = networkTableMgr;
this.tableFactory = tableFactory;
this.publicTables = publicTables;
this.serviceRegistrar = serviceRegistrar;
@@ -119,9 +122,9 @@
nodeTables = createNodeTables(suid);
edgeTables = createEdgeTables(suid);
- tableMgr.setTableMap(CyNetwork.class, this, netTables);
- tableMgr.setTableMap(CyNode.class, this, nodeTables);
- tableMgr.setTableMap(CyEdge.class, this, edgeTables);
+ networkTableMgr.setTableMap(CyNetwork.class, this, netTables);
+ networkTableMgr.setTableMap(CyNode.class, this, nodeTables);
+ networkTableMgr.setTableMap(CyEdge.class, this, edgeTables);
eventHelper = eh;
@@ -917,9 +920,9 @@
final ArraySubGraph sub = new
ArraySubGraph(this,newSUID,newId,eventHelper,newNetTable,newNodeTable,newEdgeTable,tableMgr);
serviceRegistrar.registerAllServices(sub, new Properties());
subNetworks.add(sub);
- tableMgr.setTableMap(CyNetwork.class, sub, newNetTable);
- tableMgr.setTableMap(CyNode.class, sub, newNodeTable);
- tableMgr.setTableMap(CyEdge.class, sub, newEdgeTable);
+ networkTableMgr.setTableMap(CyNetwork.class, sub, newNetTable);
+ networkTableMgr.setTableMap(CyNode.class, sub, newNodeTable);
+ networkTableMgr.setTableMap(CyEdge.class, sub, newEdgeTable);
return sub;
}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -31,7 +31,6 @@
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.model.CyTableManager;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.service.util.CyServiceRegistrar;
@@ -44,6 +43,7 @@
private final CyEventHelper help;
private final CyTableManagerImpl mgr;
+ private final CyNetworkTableManagerImpl networkTableMgr;
private final CyTableFactory tableFactory;
private final CyServiceRegistrar serviceRegistrar;
@@ -53,6 +53,7 @@
* @param help An instance of CyEventHelper.
*/
public CyNetworkFactoryImpl(final CyEventHelper help, final
CyTableManagerImpl mgr,
+ final CyNetworkTableManagerImpl
networkTableMgr,
final CyTableFactory tableFactory,
final CyServiceRegistrar serviceRegistrar)
{
@@ -70,6 +71,7 @@
this.help = help;
this.mgr = mgr;
+ this.networkTableMgr = networkTableMgr;
this.tableFactory = tableFactory;
this.serviceRegistrar = serviceRegistrar;
}
@@ -79,7 +81,7 @@
*/
@Override
public CyNetwork getInstance() {
- ArrayGraph net = new ArrayGraph(help, mgr, tableFactory,
serviceRegistrar, true);
+ ArrayGraph net = new ArrayGraph(help, mgr, networkTableMgr,
tableFactory, serviceRegistrar, true);
logger.info("CyNetwork w/ public tables created: ID = " +
net.getSUID());
logger.info("CyNetwork w/ public tables created: Base Graph ID
= " + net.getBaseNetwork().getSUID());
return net.getBaseNetwork();
@@ -90,7 +92,7 @@
*/
@Override
public CyNetwork getInstanceWithPrivateTables() {
- ArrayGraph net = new ArrayGraph(help, mgr, tableFactory,
serviceRegistrar, false);
+ ArrayGraph net = new ArrayGraph(help, mgr, networkTableMgr,
tableFactory, serviceRegistrar, false);
logger.info("CyNetwork w/ private tables created: ID = " +
net.getSUID());
logger.info("CyNetwork w/ private tables created: Base Graph ID
= " + net.getBaseNetwork().getSUID());
return net.getBaseNetwork();
Added:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkTableManagerImpl.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkTableManagerImpl.java
(rev 0)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkTableManagerImpl.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -0,0 +1,178 @@
+package org.cytoscape.model.internal;
+
+import java.lang.ref.Reference;
+import java.lang.ref.WeakReference;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.WeakHashMap;
+
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkTableManager;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.events.NetworkAboutToBeDestroyedEvent;
+import org.cytoscape.model.events.NetworkAboutToBeDestroyedListener;
+
+public class CyNetworkTableManagerImpl implements CyNetworkTableManager,
NetworkAboutToBeDestroyedListener {
+
+ Map<CyNetwork, Map<Class<? extends CyTableEntry>, Reference<Map<String,
CyTable>>>> tables;
+
+ public CyNetworkTableManagerImpl() {
+ // Use WeakReferences for CyNetworks because we can't get
notified
+ // when detached networks are no longer in use. Use
WeakReferences
+ // for the CyTable maps too because CyNetworks may be holding a
+ // reference to them. This set up allows us to automatically
clean
+ // up this map whenever CyNetworks get garbage collected.
+ tables = new WeakHashMap<CyNetwork, Map<Class<? extends
CyTableEntry>, Reference<Map<String, CyTable>>>>();
+ }
+
+ @Override
+ public void setTable(CyNetwork network, Class<? extends CyTableEntry>
type,
+ String namespace, CyTable table) {
+ if (network == null) {
+ throw new IllegalArgumentException("network cannot be
null");
+ }
+ if (type == null) {
+ throw new IllegalArgumentException("type cannot be
null");
+ }
+ if (namespace == null) {
+ throw new IllegalArgumentException("namespace cannot be
null");
+ }
+ if (table == null) {
+ throw new IllegalArgumentException("table cannot be
null");
+ }
+
+ if (namespace.equals(CyNetwork.DEFAULT_ATTRS)) {
+ throw new IllegalArgumentException("cannot overwrite
default tables");
+ }
+
+ Map<Class<? extends CyTableEntry>, Reference<Map<String,
CyTable>>> byType = tables.get(network);
+ if (byType == null) {
+ throw new IllegalStateException("network table maps are
missing for network: " + network);
+ }
+ Reference<Map<String, CyTable>> reference = byType.get(type);
+ if (reference == null) {
+ throw new IllegalStateException("network table maps are
missing for network: " + network);
+ }
+ Map<String, CyTable> byNamespace = reference.get();
+ if (byNamespace == null) {
+ throw new IllegalStateException("network table maps are
missing for network: " + network);
+ }
+ byNamespace.put(namespace, table);
+ }
+
+ @Override
+ public CyTable getTable(CyNetwork network,
+ Class<? extends CyTableEntry> type, String namespace) {
+ Map<Class<? extends CyTableEntry>, Reference<Map<String,
CyTable>>> byType = tables.get(network);
+ if (network == null) {
+ throw new IllegalArgumentException("network cannot be
null");
+ }
+ if (type == null) {
+ throw new IllegalArgumentException("type cannot be
null");
+ }
+ if (namespace == null) {
+ throw new IllegalArgumentException("namespace cannot be
null");
+ }
+
+ if (byType == null) {
+ return null;
+ }
+ Reference<Map<String, CyTable>> reference = byType.get(type);
+ if (reference == null) {
+ return null;
+ }
+ Map<String, CyTable> byNamespace = reference.get();
+ if (byNamespace == null) {
+ return null;
+ }
+ return byNamespace.get(namespace);
+ }
+
+ @Override
+ public void removeTable(CyNetwork network,
+ Class<? extends CyTableEntry> type, String namespace) {
+ if (network == null) {
+ throw new IllegalArgumentException("network cannot be
null");
+ }
+ if (type == null) {
+ throw new IllegalArgumentException("type cannot be
null");
+ }
+ if (namespace == null) {
+ throw new IllegalArgumentException("namespace cannot be
null");
+ }
+
+ if (namespace.equals(CyNetwork.DEFAULT_ATTRS)) {
+ throw new IllegalArgumentException("cannot remove
default tables");
+ }
+
+ Map<Class<? extends CyTableEntry>, Reference<Map<String,
CyTable>>> byType = tables.get(network);
+ if (byType == null) {
+ return;
+ }
+ Reference<Map<String, CyTable>> reference = byType.get(type);
+ if (reference == null) {
+ return;
+ }
+ Map<String, CyTable> byNamespace = reference.get();
+ if (byNamespace == null) {
+ return;
+ }
+ byNamespace.remove(namespace);
+ }
+
+ @Override
+ public Map<String, CyTable> getTables(CyNetwork network,
+ Class<? extends CyTableEntry> type) {
+ if (network == null) {
+ throw new IllegalArgumentException("network cannot be
null");
+ }
+ if (type == null) {
+ throw new IllegalArgumentException("type cannot be
null");
+ }
+
+ Map<Class<? extends CyTableEntry>, Reference<Map<String,
CyTable>>> byType = tables.get(network);
+ if (byType == null) {
+ return Collections.emptyMap();
+ }
+ Reference<Map<String, CyTable>> reference = byType.get(type);
+ if (reference == null) {
+ return Collections.emptyMap();
+ }
+ Map<String, CyTable> byNamespace = reference.get();
+ if (byNamespace == null) {
+ return Collections.emptyMap();
+ }
+ return Collections.unmodifiableMap(byNamespace);
+ }
+
+ @Override
+ public void reset() {
+ tables.clear();
+ }
+
+ void setTableMap(Class<? extends CyTableEntry> type, CyNetwork network,
Map<String, CyTable> tableMap) {
+ if (network == null) {
+ throw new IllegalArgumentException("network cannot be
null");
+ }
+ if (type == null) {
+ throw new IllegalArgumentException("type cannot be
null");
+ }
+ if (tableMap == null) {
+ throw new IllegalArgumentException("table map cannot be
null");
+ }
+
+ Map<Class<? extends CyTableEntry>, Reference<Map<String,
CyTable>>> byType = tables.get(network);
+ if (byType == null) {
+ byType = new HashMap<Class<? extends CyTableEntry>,
Reference<Map<String,CyTable>>>();
+ tables.put(network, byType);
+ }
+ byType.put(type, new
WeakReference<Map<String,CyTable>>(tableMap));
+ }
+
+ @Override
+ public void handleEvent(NetworkAboutToBeDestroyedEvent e) {
+ tables.remove(e.getNetwork());
+ }
+}
Property changes on:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkTableManagerImpl.java
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableManagerImpl.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableManagerImpl.java
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableManagerImpl.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -27,31 +27,30 @@
*/
package org.cytoscape.model.internal;
-import org.cytoscape.event.CyEventHelper;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTable.Mutability;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTableManager;
-import org.cytoscape.model.CyTableMetadata;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedEvent;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedListener;
import org.cytoscape.model.events.TableAboutToBeDeletedEvent;
import org.cytoscape.model.events.TableAddedEvent;
import org.cytoscape.model.events.TableDeletedEvent;
-
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
/**
* An interface describing a factory used for managing {@link CyTable} objects.
* This class will be provided as a service through Spring/OSGi.
@@ -59,7 +58,8 @@
public class CyTableManagerImpl implements CyTableManager,
NetworkAboutToBeDestroyedListener {
private static final Logger logger =
LoggerFactory.getLogger(CyTableManagerImpl.class);
private final CyEventHelper eventHelper;
- private final Map<Class<?>, Map<CyNetwork, Map<String, CyTable>>>
networkTableMap;
+ private final CyNetworkTableManager networkTableManager;
+ private final CyNetworkManager networkManager;
private final Map<Long, CyTable> tables;
/**
@@ -67,14 +67,11 @@
*
* @param eventHelper DOCUMENT ME!
*/
- public CyTableManagerImpl(final CyEventHelper eventHelper) {
+ public CyTableManagerImpl(final CyEventHelper eventHelper,
CyNetworkTableManager networkTableManager, CyNetworkManager networkManager) {
this.eventHelper = eventHelper;
-
- networkTableMap = new HashMap<Class<?>, Map<CyNetwork,
Map<String, CyTable>>>();
- networkTableMap.put(CyNetwork.class, new HashMap<CyNetwork,
Map<String, CyTable>>());
- networkTableMap.put(CyNode.class, new HashMap<CyNetwork,
Map<String, CyTable>>());
- networkTableMap.put(CyEdge.class, new HashMap<CyNetwork,
Map<String, CyTable>>());
-
+ this.networkTableManager = networkTableManager;
+ this.networkManager = networkManager;
+
tables = new HashMap<Long, CyTable>();
}
@@ -83,100 +80,13 @@
*/
@Override
public synchronized void reset() {
- networkTableMap.clear();
+// networkTableMap.clear();
tables.clear();
}
/**
* DOCUMENT ME!
*
- * @param graphObjectType DOCUMENT ME!
- * @param network DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public synchronized Map<String, CyTable> getTableMap(final Class<?>
graphObjectType,
- final CyNetwork
network) {
- if ((network == null) || (graphObjectType == null)) {
- return null;
- }
-
- Map<CyNetwork, Map<String, CyTable>> tmap =
networkTableMap.get(graphObjectType);
-
- if (tmap == null) {
- throw new IllegalArgumentException("no data tables of
type: " + graphObjectType
- + " exist");
- }
-
- return tmap.get(network);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param graphObjectType DOCUMENT ME!
- * @param network DOCUMENT ME!
- * @param table DOCUMENT ME!
- */
- public void addNetworkTable(Class<?> graphObjectType, final CyNetwork
network,
- final CyTable table) {
- if (network == null) {
- throw new NullPointerException("CyNetwork is null");
- }
-
- if (graphObjectType == null) {
- throw new NullPointerException("Type is null");
- }
-
- if (table == null) {
- throw new NullPointerException("Table is null");
- }
-
- if (!networkTableMap.containsKey(graphObjectType)) {
- networkTableMap.put(graphObjectType, new
HashMap<CyNetwork, Map<String, CyTable>>());
- }
-
- Map<CyNetwork, Map<String, CyTable>> tmap =
networkTableMap.get(graphObjectType);
- Map<String, CyTable> tm = new HashMap<String, CyTable>();
- tm.put(CyNetwork.DEFAULT_ATTRS, table);
-
- tmap.put(network, tm);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param graphObjectType DOCUMENT ME!
- * @param network DOCUMENT ME!
- * @param tm DOCUMENT ME!
- */
- public synchronized void setTableMap(final Class<?> graphObjectType,
final CyNetwork network,
- final Map<String, CyTable> tm) {
- if (network == null) {
- throw new NullPointerException("CyNetwork is null");
- }
-
- if (graphObjectType == null) {
- throw new NullPointerException("Type is null");
- }
-
- if (!networkTableMap.containsKey(graphObjectType)) {
- networkTableMap.put(graphObjectType, new
HashMap<CyNetwork, Map<String, CyTable>>());
- }
-
- Map<CyNetwork, Map<String, CyTable>> tmap =
networkTableMap.get(graphObjectType);
-
- if (tm == null) {
- tmap.remove(network);
- } else {
- tmap.put(network, tm);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
* @param t DOCUMENT ME!
*/
public synchronized void addTable(final CyTable t) {
@@ -196,51 +106,18 @@
* @return DOCUMENT ME!
*/
@Override
- public synchronized Set<CyTableMetadata> getAllTables(final boolean
includePrivate) {
- Set<CyTableMetadata> res = new HashSet<CyTableMetadata>();
+ public synchronized Set<CyTable> getAllTables(final boolean
includePrivate) {
+ Set<CyTable> res = new HashSet<CyTable>();
for (Long key : tables.keySet()) {
if (includePrivate || tables.get(key).isPublic()) {
- res.add(createMetadata(tables.get(key)));
+ res.add(tables.get(key));
}
}
return res;
}
- private CyTableMetadata createMetadata(CyTable cyTable) {
- Class<?> entryType = null;
- String entryNamespace = null;
- Set<CyNetwork> networks = new HashSet<CyNetwork>();
-
- for (Entry<Class<?>, Map<CyNetwork, Map<String, CyTable>>>
mapEntry : networkTableMap
-
.entrySet()) {
- Class<?> type = mapEntry.getKey();
- Map<CyNetwork, Map<String, CyTable>> networkMap =
mapEntry.getValue();
-
- for (Entry<CyNetwork, Map<String, CyTable>> entry :
networkMap.entrySet()) {
- CyNetwork network = entry.getKey();
-
- for (Entry<String, CyTable> tableEntry :
entry.getValue().entrySet()) {
- String namespace = tableEntry.getKey();
- CyTable table = tableEntry.getValue();
-
- if (table.getSUID() ==
cyTable.getSUID()) {
- entryType = type;
- entryNamespace = namespace;
- networks.add(network);
- }
- }
- }
- }
-
- if (networks.size() > 0) {
- return new CyTableMetadataImpl(entryType, cyTable,
networks, entryNamespace);
- }
-
- return new CyTableMetadataImpl(null, cyTable, networks, null);
- }
-
/**
* DOCUMENT ME!
*
@@ -287,33 +164,37 @@
table = null;
}
- private static final Class[] tableTypes = new Class[] {
- CyNetwork.class,
CyNode.class, CyEdge.class
- };
-
/**
* DOCUMENT ME!
*
- * @param e DOCUMENT ME!
+ * @param suid DOCUMENT ME!
*/
@Override
+ public void deleteTable(long suid) {
+ deleteTableInternal(suid, false);
+ }
+
+ @Override
public void handleEvent(NetworkAboutToBeDestroyedEvent e) {
+ // Collect set of tables to dispose
CyNetwork network = e.getNetwork();
-
- for (Class<?> type : tableTypes) {
- for (CyTable table : getTableMap(type,
network).values()) {
- deleteTableInternal(table.getSUID(), true);
+ Set<CyTable> tablesToDispose = new HashSet<CyTable>();
+ for (Class<? extends CyTableEntry> type : new Class[] {
CyNetwork.class, CyNode.class, CyEdge.class }) {
+
tablesToDispose.addAll(networkTableManager.getTables(network, type).values());
+ }
+
+ // Exclude tables that are being referenced by other networks
+ for (CyNetwork otherNetwork : networkManager.getNetworkSet()) {
+ if (otherNetwork.getSUID() == network.getSUID()) {
+ continue;
}
+ for (Class<? extends CyTableEntry> type : new Class[] {
CyNetwork.class, CyNode.class, CyEdge.class }) {
+
tablesToDispose.removeAll(networkTableManager.getTables(otherNetwork,
type).values());
+ }
}
+
+ for (CyTable table : tablesToDispose) {
+ deleteTableInternal(table.getSUID(), true);
+ }
}
-
- /**
- * DOCUMENT ME!
- *
- * @param suid DOCUMENT ME!
- */
- @Override
- public void deleteTable(long suid) {
- deleteTableInternal(suid, false);
- }
}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableMetadataImpl.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableMetadataImpl.java
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableMetadataImpl.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -1,7 +1,5 @@
package org.cytoscape.model.internal;
-import java.util.Set;
-
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableMetadata;
@@ -10,13 +8,13 @@
private final Class<?> type;
private final CyTable table;
- private final Set<CyNetwork> networks;
+ private final CyNetwork network;
private final String namespace;
- public CyTableMetadataImpl(Class<?> type, CyTable table, Set<CyNetwork>
networks, String namespace) {
+ public CyTableMetadataImpl(Class<?> type, CyTable table, CyNetwork
network, String namespace) {
this.type = type;
this.table = table;
- this.networks = networks;
+ this.network = network;
this.namespace = namespace;
}
@@ -31,8 +29,8 @@
}
@Override
- public Set<CyNetwork> getCyNetworks() {
- return networks;
+ public CyNetwork getCyNetwork() {
+ return network;
}
@Override
Modified:
core3/impl/trunk/model-impl/impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/impl/trunk/model-impl/impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-09-20 18:00:53 UTC (rev 26881)
@@ -35,6 +35,13 @@
</osgi:interfaces>
</osgi:service>
+ <osgi:service id="cyNetworkTableManagerService"
+ ref="cyNetworkTableManager">
+ <osgi:interfaces>
+ <value>org.cytoscape.model.CyNetworkTableManager</value>
+ </osgi:interfaces>
+ </osgi:service>
+
<osgi:service id="cyNetworkManagerService"
ref="cyNetworkManager"
interface="org.cytoscape.model.CyNetworkManager">
</osgi:service>
Modified:
core3/impl/trunk/model-impl/impl/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/impl/trunk/model-impl/impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-20 18:00:53 UTC (rev 26881)
@@ -17,8 +17,13 @@
<bean id="cyTableManager"
class="org.cytoscape.model.internal.CyTableManagerImpl">
<constructor-arg ref="cyEventHelperServiceRef" />
+ <constructor-arg ref="cyNetworkTableManager" />
+ <constructor-arg ref="cyNetworkManager" />
</bean>
+ <bean id="cyNetworkTableManager"
class="org.cytoscape.model.internal.CyNetworkTableManagerImpl">
+ </bean>
+
<bean id="cyTableFactory"
class="org.cytoscape.model.internal.CyTableFactoryImpl">
<constructor-arg ref="cyEventHelperServiceRef" />
<constructor-arg ref="InterpreterRef" />
@@ -28,6 +33,7 @@
<bean id="cyNetworkFactory"
class="org.cytoscape.model.internal.CyNetworkFactoryImpl">
<constructor-arg ref="cyEventHelperServiceRef" />
<constructor-arg ref="cyTableManager" />
+ <constructor-arg ref="cyNetworkTableManager" />
<constructor-arg ref="cyTableFactory" />
<constructor-arg ref="cyServiceRegistrarServiceRef" />
</bean>
Added:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkTableManagerTest.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkTableManagerTest.java
(rev 0)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkTableManagerTest.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -0,0 +1,76 @@
+/*
+ Copyright (c) 2008, 2010-2011, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library 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. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.model;
+
+
+import static org.junit.Assert.*;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import org.cytoscape.equations.Interpreter;
+import org.cytoscape.equations.internal.interpreter.InterpreterImpl;
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.event.DummyCyEventHelper;
+import org.cytoscape.model.Identifiable;
+import org.cytoscape.model.CyTable.SavePolicy;
+import org.cytoscape.model.internal.ArrayGraph;
+import org.cytoscape.model.internal.CyNetworkTableManagerImpl;
+import org.cytoscape.model.internal.CyTableFactoryImpl;
+import org.cytoscape.model.internal.CyTableImpl;
+import org.cytoscape.model.internal.CyTableManagerImpl;
+import org.cytoscape.service.util.CyServiceRegistrar;
+
+import static org.mockito.Mockito.*;
+
+
+public class CyNetworkTableManagerTest extends
AbstractCyNetworkTableManagerTest {
+ CyTableManagerImpl mgrImpl;
+ CyNetworkTableManagerImpl networkTableMgr;
+
+ @Before
+ public void setUp() {
+ super.setUp();
+ CyEventHelper eh = new DummyCyEventHelper();
+ mgrImpl = new CyTableManagerImpl(eh, networkTableMgr, null);
+ networkTableMgr = new CyNetworkTableManagerImpl();
+ mgr = networkTableMgr;
+ final Interpreter interpreter = new InterpreterImpl();
+ final CyServiceRegistrar serviceRegistrar =
mock(CyServiceRegistrar.class);
+ goodNetwork =
+ new ArrayGraph(eh, mgrImpl, networkTableMgr,
+ new CyTableFactoryImpl(eh, interpreter,
serviceRegistrar),
+ serviceRegistrar, true).getBaseNetwork();
+ }
+
+ @After
+ public void tearDown() {
+ mgr = null;
+ goodNetwork = null;
+ }
+}
Property changes on:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkTableManagerTest.java
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Modified:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -40,6 +40,7 @@
import org.cytoscape.model.Identifiable;
import org.cytoscape.model.CyTable.SavePolicy;
import org.cytoscape.model.internal.ArrayGraph;
+import org.cytoscape.model.internal.CyNetworkTableManagerImpl;
import org.cytoscape.model.internal.CyTableFactoryImpl;
import org.cytoscape.model.internal.CyTableImpl;
import org.cytoscape.model.internal.CyTableManagerImpl;
@@ -50,17 +51,19 @@
public class CyTableManagerTest extends AbstractCyTableManagerTest {
CyTableManagerImpl mgrImpl;
+ CyNetworkTableManagerImpl networkTableMgr;
@Before
public void setUp() {
super.setUp();
CyEventHelper eh = new DummyCyEventHelper();
- mgrImpl = new CyTableManagerImpl(eh);
+ networkTableMgr = new CyNetworkTableManagerImpl();
+ mgrImpl = new CyTableManagerImpl(eh, networkTableMgr, null);
mgr = mgrImpl;
final Interpreter interpreter = new InterpreterImpl();
final CyServiceRegistrar serviceRegistrar =
mock(CyServiceRegistrar.class);
goodNetwork =
- new ArrayGraph(eh, mgrImpl,
+ new ArrayGraph(eh, mgrImpl, networkTableMgr,
new CyTableFactoryImpl(eh, interpreter,
serviceRegistrar),
serviceRegistrar, true).getBaseNetwork();
}
Modified:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/NetworkTestSupport.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/NetworkTestSupport.java
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/NetworkTestSupport.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -6,9 +6,9 @@
import org.cytoscape.event.DummyCyEventHelper;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.internal.CyNetworkFactoryImpl;
+import org.cytoscape.model.internal.CyNetworkTableManagerImpl;
import org.cytoscape.model.internal.CyTableFactoryImpl;
import org.cytoscape.model.internal.CyTableManagerImpl;
import org.cytoscape.service.util.CyServiceRegistrar;
@@ -21,15 +21,17 @@
protected CyNetworkFactory networkFactory;
protected CyEventHelper eventHelper;
protected CyTableManagerImpl tableMgr;
+ protected CyNetworkTableManagerImpl networkTableMgr;
public NetworkTestSupport() {
eventHelper = new DummyCyEventHelper();
tableMgr = mock(CyTableManagerImpl.class);
+ networkTableMgr = mock(CyNetworkTableManagerImpl.class);
final CyServiceRegistrar serviceRegistrar =
mock(CyServiceRegistrar.class);
final CyTableFactoryImpl tableFactory =
new CyTableFactoryImpl(eventHelper,
mock(Interpreter.class), serviceRegistrar);
networkFactory =
- new CyNetworkFactoryImpl(eventHelper, tableMgr,
tableFactory,
+ new CyNetworkFactoryImpl(eventHelper, tableMgr,
networkTableMgr, tableFactory,
serviceRegistrar);
}
Modified:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -28,21 +28,23 @@
package org.cytoscape.model;
-import org.cytoscape.event.DummyCyEventHelper;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.mockito.Mockito.mock;
+
import org.cytoscape.equations.Interpreter;
import org.cytoscape.equations.internal.interpreter.InterpreterImpl;
+import org.cytoscape.event.DummyCyEventHelper;
import org.cytoscape.model.internal.ArrayGraph;
+import org.cytoscape.model.internal.CyNetworkTableManagerImpl;
+import org.cytoscape.model.internal.CyTableFactoryImpl;
import org.cytoscape.model.internal.CyTableManagerImpl;
-import org.cytoscape.model.internal.CyTableFactoryImpl;
import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.service.util.CyServiceRegistrar;
-
import org.junit.Test;
-import static org.junit.Assert.*;
-import static org.mockito.Mockito.*;
-
public class TestCyNetworkFactory {
public TestCyNetworkFactory() { }
@@ -56,22 +58,24 @@
public static CyRootNetwork getPublicRootInstance() {
DummyCyEventHelper deh = new DummyCyEventHelper();
- CyTableManagerImpl tm = new CyTableManagerImpl(deh);
+ CyNetworkTableManagerImpl ntm = new CyNetworkTableManagerImpl();
+ CyTableManagerImpl tm = new CyTableManagerImpl(deh, ntm, null);
Interpreter interp = new InterpreterImpl();
final CyServiceRegistrar serviceRegistrar =
mock(CyServiceRegistrar.class);
ArrayGraph ar =
- new ArrayGraph(deh, tm, new CyTableFactoryImpl(deh,
interp, serviceRegistrar),
+ new ArrayGraph(deh, tm, ntm, new
CyTableFactoryImpl(deh, interp, serviceRegistrar),
serviceRegistrar, true);
return ar;
}
public static CyRootNetwork getPrivateRootInstance() {
DummyCyEventHelper deh = new DummyCyEventHelper();
- CyTableManagerImpl tm = new CyTableManagerImpl(deh);
+ CyNetworkTableManagerImpl ntm = new CyNetworkTableManagerImpl();
+ CyTableManagerImpl tm = new CyTableManagerImpl(deh, ntm, null);
Interpreter interp = new InterpreterImpl();
final CyServiceRegistrar serviceRegistrar =
mock(CyServiceRegistrar.class);
ArrayGraph ar =
- new ArrayGraph(deh, tm, new CyTableFactoryImpl(deh,
interp, serviceRegistrar),
+ new ArrayGraph(deh, tm, ntm, new
CyTableFactoryImpl(deh, interp, serviceRegistrar),
serviceRegistrar, false);
return ar;
}
Modified:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/subnetwork/CySubNetworkCyTableManagerTest.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/subnetwork/CySubNetworkCyTableManagerTest.java
2011-09-20 17:50:48 UTC (rev 26880)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/subnetwork/CySubNetworkCyTableManagerTest.java
2011-09-20 18:00:53 UTC (rev 26881)
@@ -28,23 +28,20 @@
package org.cytoscape.model.subnetwork;
-import java.util.Map;
+import static org.mockito.Mockito.mock;
-import org.cytoscape.model.internal.CyTableManagerImpl;
-import org.cytoscape.model.internal.CyTableFactoryImpl;
-import org.cytoscape.model.internal.ArrayGraph;
import org.cytoscape.equations.Interpreter;
import org.cytoscape.equations.internal.interpreter.InterpreterImpl;
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.event.DummyCyEventHelper;
import org.cytoscape.model.AbstractCyTableManagerTest;
+import org.cytoscape.model.internal.ArrayGraph;
+import org.cytoscape.model.internal.CyNetworkTableManagerImpl;
+import org.cytoscape.model.internal.CyTableFactoryImpl;
+import org.cytoscape.model.internal.CyTableManagerImpl;
import org.cytoscape.service.util.CyServiceRegistrar;
-import org.junit.Test;
-import static org.mockito.Mockito.*;
-
-
/**
* The purpose of this test is to validate that everything that holds true
* for CyNetworks in CyTableManager also holds true for CySubNetworks!
@@ -53,12 +50,13 @@
public void setUp() {
super.setUp();
CyEventHelper eh = new DummyCyEventHelper();
- CyTableManagerImpl mgrImpl = new CyTableManagerImpl(eh);
+ CyNetworkTableManagerImpl networkMgrImpl = new
CyNetworkTableManagerImpl();
+ CyTableManagerImpl mgrImpl = new CyTableManagerImpl(eh,
networkMgrImpl, null);
mgr = mgrImpl;
final Interpreter interpreter = new InterpreterImpl();
final CyServiceRegistrar serviceRegistrar =
mock(CyServiceRegistrar.class);
ArrayGraph baseNet =
- new ArrayGraph(eh, mgrImpl,
+ new ArrayGraph(eh, mgrImpl, networkMgrImpl,
new CyTableFactoryImpl(eh, interpreter,
serviceRegistrar),
serviceRegistrar, true);
// This is a different subnetwork and not "baseNetwork" in
ArrayGraph.
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