Author: clopes
Date: 2012-08-08 11:02:21 -0700 (Wed, 08 Aug 2012)
New Revision: 30125
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/SUIDUpdater.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/ObjectTypeMap.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleListAttribute.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/SUIDUpdaterTest.java
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
Log:
Fixed SUIDUpdater to work with shared/local tables.
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
2012-08-08 17:55:49 UTC (rev 30124)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
2012-08-08 18:02:21 UTC (rev 30125)
@@ -189,7 +189,7 @@
UnrecognizedVisualPropertyManager
unrecognizedVisualPropertyManager = new
UnrecognizedVisualPropertyManager(cyTableFactoryServiceRef,cyTableManagerServiceRef);
GMLNetworkReaderFactory gmlNetworkViewReaderFactory = new
GMLNetworkReaderFactory(gmlFilter,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,renderingEngineManagerServiceRef,unrecognizedVisualPropertyManager);
- ReadCache readCache = new ReadCache();
+ ReadCache readCache = new
ReadCache(cyNetworkTableManagerServiceRef);
SUIDUpdater suidUpdater = new SUIDUpdater();
ReadDataManager readDataManager = new
ReadDataManager(readCache,suidUpdater,equationCompilerServiceRef,cyNetworkFactoryServiceRef,cyRootNetworkManagerServiceRef);
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/SUIDUpdater.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/SUIDUpdater.java
2012-08-08 17:55:49 UTC (rev 30124)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/SUIDUpdater.java
2012-08-08 18:02:21 UTC (rev 30125)
@@ -1,12 +1,12 @@
package org.cytoscape.io.internal.read;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import java.util.WeakHashMap;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyRow;
@@ -18,10 +18,10 @@
*/
public class SUIDUpdater {
- private static final String SUID_COLUMN_SUFFIX = ".SUID";
+ public static final String SUID_COLUMN_SUFFIX = ".SUID";
private Map<Long/*old SUID*/, Long/*new SUID*/> suidMap;
- private Map<CyTable, Set<String>/*column names*/> suidColumnMap;
+ private Set<CyTable> tables;
public SUIDUpdater() {
init();
@@ -29,7 +29,7 @@
public void init() {
suidMap = new HashMap<Long, Long>();
- suidColumnMap = new WeakHashMap<CyTable, Set<String>>();
+ tables = new HashSet<CyTable>();
}
public void addSUIDMapping(final Long oldSUID, final Long newSUID) {
@@ -37,46 +37,57 @@
suidMap.put(oldSUID, newSUID);
}
- public Long getNewSUID(final Long oldSUID) {
- return suidMap.get(oldSUID);
+ public void addTable(final CyTable table) {
+ tables.add(table);
}
- public void addSUIDColumn(final CyTable table, final String name) {
- Set<String> columnNames = suidColumnMap.get(table);
-
- if (columnNames == null) {
- columnNames = new HashSet<String>();
- suidColumnMap.put(table, columnNames);
- }
-
- columnNames.add(name);
+ public void addTables(final Set<CyTable> networkTables) {
+ if (networkTables != null)
+ tables.addAll(networkTables);
}
public void updateSUIDColumns() {
- for (final Map.Entry<CyTable, Set<String>> entry :
suidColumnMap.entrySet()) {
- final CyTable tbl = entry.getKey();
- final Set<String> columnNames = entry.getValue();
+ final Set<CyColumn> updated = new HashSet<CyColumn>();
+
+ for (final CyTable tbl : tables) {
+ final Collection<CyColumn> columns = tbl.getColumns();
- for (final String name : columnNames)
- updateRows(tbl, name);
+ for (final CyColumn c : columns) {
+ if (isUpdatableSUIDColumn(c) &&
!updated.contains(c)) {
+ updateRows(tbl, c);
+ updated.add(c);
+ }
+ }
}
}
+ public static boolean isUpdatableSUIDColumn(final CyColumn column) {
+ if (column != null
+ && !column.isPrimaryKey()
+ && !column.getVirtualColumnInfo().isVirtual()
+ && (column.getType() == Long.class ||
+
(Collection.class.isAssignableFrom(column.getType()) &&
+
column.getListElementType() == Long.class)))
+ return isUpdatableSUIDColumnName(column.getName());
+
+ return false;
+ }
+
+ public static boolean isUpdatableSUIDColumnName(final String
columnName) {
+ return columnName != null &&
columnName.endsWith(SUID_COLUMN_SUFFIX);
+ }
+
public void dispose() {
init();
}
- public static boolean isUpdatableSUIDColumn(final String columnName) {
- return columnName != null && columnName.endsWith(SUID_COLUMN_SUFFIX);
- }
-
@Override
public String toString() {
- return "SUIDUpdater{ suidMap=" + suidMap + ", suidColumnMap=" +
suidColumnMap + " }";
+ return "SUIDUpdater{ suidMap=" + suidMap + ", tables=" + tables
+ " }";
}
-
- private void updateRows(final CyTable tbl, final String columnName) {
- final CyColumn column = tbl.getColumn(columnName);
+
+ private void updateRows(final CyTable tbl, final CyColumn column) {
+ final String columnName = column.getName();
final Class<?> type = column.getType();
final Class<?> listType = column.getListElementType();
@@ -106,4 +117,8 @@
}
}
}
+
+ private Long getNewSUID(final Long oldSUID) {
+ return suidMap.get(oldSUID);
+ }
}
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
2012-08-08 17:55:49 UTC (rev 30124)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
2012-08-08 18:02:21 UTC (rev 30125)
@@ -300,7 +300,7 @@
builderFilenameMap.put(builder, filename);
// Look for SUID-type columns--only global tables now
- findSUIDColumns(table);
+ suidUpdater.addTable(table);
}
}
@@ -500,12 +500,12 @@
networkTableMgr.setTable(network, type, namespace, src);
builder.setCyTable(src);
- findSUIDColumns(src);
+ suidUpdater.addTable(src);
} else {
mergeTables(src, tgt, type);
builder.setCyTable(tgt);
- findSUIDColumns(tgt);
+ suidUpdater.addTable(tgt);
}
}
@@ -561,13 +561,6 @@
}
}
- private void findSUIDColumns(final CyTable table) {
- for (final CyColumn column : table.getColumns()) {
- if (SUIDUpdater.isUpdatableSUIDColumn(column.getName()))
- suidUpdater.addSUIDColumn(table,
column.getName());
- }
- }
-
private void updateSUIDColumns() {
suidUpdater.updateSUIDColumns();
}
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/ObjectTypeMap.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/ObjectTypeMap.java
2012-08-08 17:55:49 UTC (rev 30124)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/ObjectTypeMap.java
2012-08-08 18:02:21 UTC (rev 30125)
@@ -44,7 +44,7 @@
break;
case REAL:
if (value != null) {
- if (SUIDUpdater.isUpdatableSUIDColumn(name))
+ if (SUIDUpdater.isUpdatableSUIDColumnName(name))
typedValue = new Long(value);
else
typedValue = new Double(value);
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2012-08-08 17:55:49 UTC (rev 30124)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2012-08-08 18:02:21 UTC (rev 30125)
@@ -251,7 +251,7 @@
break;
case REAL:
if (name != null) {
- if
(SUIDUpdater.isUpdatableSUIDColumn(name))
+ if
(SUIDUpdater.isUpdatableSUIDColumnName(name))
setAttribute(row, name,
Long.class, (Long) value);
else
setAttribute(row, name,
Double.class, (Double) value);
@@ -276,9 +276,6 @@
if (column != null &&
List.class.isAssignableFrom(column.getType()))
row.set(name, null);
- if (SUIDUpdater.isUpdatableSUIDColumn(name))
- manager.getSUIDUpdater().addSUIDColumn(row.getTable(),
name);
-
return ParseState.LIST_ATT;
}
@@ -299,9 +296,6 @@
if (value != null) {
row.set(name, value);
-
- if (SUIDUpdater.isUpdatableSUIDColumn(name))
- manager.getSUIDUpdater().addSUIDColumn(row.getTable(),
name);
}
}
}
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone.java
2012-08-08 17:55:49 UTC (rev 30124)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone.java
2012-08-08 18:02:21 UTC (rev 30125)
@@ -30,6 +30,7 @@
import java.util.Map;
import java.util.Set;
+import org.cytoscape.io.internal.read.SUIDUpdater;
import org.cytoscape.io.internal.read.xgmml.ParseState;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
@@ -144,7 +145,9 @@
private void updateSUIDAttributes() {
if (!manager.isSessionFormat()) {
- manager.getSUIDUpdater().updateSUIDColumns();
+ final SUIDUpdater updater = manager.getSUIDUpdater();
+
updater.addTables(manager.getCache().getNetworkTables());
+ updater.updateSUIDColumns();
}
}
}
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleListAttribute.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleListAttribute.java
2012-08-08 17:55:49 UTC (rev 30124)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleListAttribute.java
2012-08-08 18:02:21 UTC (rev 30125)
@@ -53,7 +53,7 @@
clazz = Boolean.class;
break;
case REAL:
- clazz = SUIDUpdater.isUpdatableSUIDColumn(name) ? Long.class :
Double.class;
+ clazz = SUIDUpdater.isUpdatableSUIDColumnName(name) ?
Long.class : Double.class;
break;
case INTEGER:
clazz = Integer.class;
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
2012-08-08 17:55:49 UTC (rev 30124)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
2012-08-08 18:02:21 UTC (rev 30125)
@@ -28,6 +28,7 @@
package org.cytoscape.io.internal.util;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.WeakHashMap;
@@ -35,7 +36,10 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.subnetwork.CySubNetwork;
import org.cytoscape.view.model.CyNetworkView;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -58,8 +62,15 @@
private Map<CyNetwork, Set<Long>> edgeLinkMap;
private Map<CyNode, Object/*network's id*/> networkPointerMap;
+ private final CyNetworkTableManager netTblMgr;
+
private static final Logger logger =
LoggerFactory.getLogger(ReadCache.class);
+
+ public ReadCache(final CyNetworkTableManager netTblMgr) {
+ this.netTblMgr = netTblMgr;
+ }
+
public void init() {
oldIdMap = new HashMap<Long, Object>();
nodeByIdMap = new HashMap<Object, CyNode>();
@@ -197,6 +208,34 @@
return nodeByNameMap;
}
+ public Set<CyTable> getNetworkTables() {
+ final Set<CyTable> tables = new HashSet<CyTable>();
+ final Set<CyNetwork> networks = new HashSet<CyNetwork>();
+ final Class<?>[] types = new Class[] { CyNetwork.class,
CyNode.class, CyEdge.class };
+
+ if (networkByIdMap.values() != null)
+ networks.addAll(networkByIdMap.values());
+
+ for (final CyNetwork n : networks) {
+ for (final Class t : types) {
+ Map<String, CyTable> tabMap =
netTblMgr.getTables(n, t);
+
+ if (tabMap != null)
+ tables.addAll(tabMap.values());
+
+ if (n instanceof CySubNetwork) {
+ // Don't forget the root-network tables.
+ tabMap =
netTblMgr.getTables(((CySubNetwork) n).getRootNetwork(), t);
+
+ if (tabMap != null)
+ tables.addAll(tabMap.values());
+ }
+ }
+ }
+
+ return tables;
+ }
+
public void createNetworkPointers() {
if (networkPointerMap != null) {
// Iterate the rows and recreate the network pointers
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/SUIDUpdaterTest.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/SUIDUpdaterTest.java
2012-08-08 17:55:49 UTC (rev 30124)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/SUIDUpdaterTest.java
2012-08-08 18:02:21 UTC (rev 30125)
@@ -1,19 +1,155 @@
package org.cytoscape.io.internal.read;
import static org.junit.Assert.*;
+
+import java.util.List;
+
+import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyColumnTest;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.VirtualColumnInfo;
import org.junit.Test;
public class SUIDUpdaterTest {
@Test
public void testIsUpdatableSUIDColumn() {
- assertTrue(SUIDUpdater.isUpdatableSUIDColumn("name.SUID"));
- assertFalse(SUIDUpdater.isUpdatableSUIDColumn("name.suid")); //
Case sensitive!
- assertFalse(SUIDUpdater.isUpdatableSUIDColumn("name.Suid"));
- assertFalse(SUIDUpdater.isUpdatableSUIDColumn("name.id"));
- assertFalse(SUIDUpdater.isUpdatableSUIDColumn("SUID"));
- assertFalse(SUIDUpdater.isUpdatableSUIDColumn("suid"));
- assertFalse(SUIDUpdater.isUpdatableSUIDColumn(""));
- assertFalse(SUIDUpdater.isUpdatableSUIDColumn(null));
+
assertTrue(SUIDUpdater.isUpdatableSUIDColumn(newColumn("name.SUID", Long.class,
false, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn("name.SUID",
Integer.class, false, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn("name.SUID",
Double.class, false, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn("name.SUID",
String.class, false, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn("name.SUID",
Boolean.class, false, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn("name.SUID",
Long.class, true, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn("name.SUID",
Long.class, false, true)));
+
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn("name.suid",
Long.class, false, false))); // Case sensitive!
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn("name.Suid",
Long.class, false, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn("name.id", Long.class,
false, false)));
+ assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn("SUID",
Long.class, false, false)));
+ assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn("suid",
Long.class, false, false)));
+ assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn("",
Long.class, false, false)));
+ assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newColumn(null,
Long.class, false, false)));
+
+ // List column
+
assertTrue(SUIDUpdater.isUpdatableSUIDColumn(newListColumn("list.SUID",
Long.class, false, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newListColumn("list.SUID",
Integer.class, false, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newListColumn("list.SUID",
Double.class, false, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newListColumn("list.SUID",
String.class, false, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newListColumn("list.SUID",
Boolean.class, false, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newListColumn("list.SUID",
Long.class, true, false)));
+
assertFalse(SUIDUpdater.isUpdatableSUIDColumn(newListColumn("list.SUID",
Long.class, false, true)));
}
+
+ private CyColumn newColumn(final String name, final Class<?> type,
final boolean isPK, final boolean isVirtual) {
+ return new DummyColumn(name, type, null, isPK, new
DummyVirtualColumnInfo(isVirtual));
+ }
+
+ private CyColumn newListColumn(final String name, final Class<?> type,
final boolean isPK, final boolean isVirtual) {
+ return new DummyColumn(name, List.class, type, isPK, new
DummyVirtualColumnInfo(isVirtual));
+ }
+
+ static class DummyColumn implements CyColumn {
+ private String name;
+ private Class<?> type;
+ private Class<?> listType;
+ private boolean isPK;
+ private VirtualColumnInfo virtualInfo;
+
+ public DummyColumn(String name, Class<?> type, Class<?>
listType, boolean isPK, VirtualColumnInfo virtualInfo) {
+ this.name = name;
+ this.type = type;
+ this.listType = listType;
+ this.isPK = isPK;
+ this.virtualInfo = virtualInfo;
+ }
+
+ @Override
+ public void setName(String newName) {
+ this.name = newName;
+ }
+
+ @Override
+ public boolean isPrimaryKey() {
+ return isPK;
+ }
+
+ @Override
+ public boolean isImmutable() {
+ return false;
+ }
+
+ @Override
+ public VirtualColumnInfo getVirtualColumnInfo() {
+ return virtualInfo;
+ }
+
+ @Override
+ public <T> List<T> getValues(Class<? extends T> type) {
+ return null;
+ }
+
+ @Override
+ public Class<?> getType() {
+ return type;
+ }
+
+ @Override
+ public CyTable getTable() {
+ return null;
+ }
+
+ @Override
+ public String getName() {
+ return name;
+ }
+
+ @Override
+ public Class<?> getListElementType() {
+ return listType;
+ }
+
+ @Override
+ public Object getDefaultValue() {
+ return null;
+ }
+ };
+
+ private static class DummyVirtualColumnInfo implements
VirtualColumnInfo {
+
+ private final boolean isVirtual;
+
+ public DummyVirtualColumnInfo(boolean isVirtual) {
+ this.isVirtual = isVirtual;
+ }
+
+ @Override
+ public boolean isVirtual() {
+ return isVirtual;
+ }
+
+ @Override
+ public String getSourceColumn() {
+ return null;
+ }
+
+ @Override
+ public String getSourceJoinKey() {
+ return null;
+ }
+
+ @Override
+ public String getTargetJoinKey() {
+ return null;
+ }
+
+ @Override
+ public CyTable getSourceTable() {
+ return null;
+ }
+
+ @Override
+ public boolean isImmutable() {
+ return false;
+ }
+ }
}
Modified:
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
===================================================================
---
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
2012-08-08 17:55:49 UTC (rev 30124)
+++
csplugins/trunk/ucsd/mes/cy3-shared-local-tables/impl/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
2012-08-08 18:02:21 UTC (rev 30125)
@@ -8,6 +8,7 @@
import java.io.File;
import java.io.FileInputStream;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
import org.cytoscape.ding.NetworkViewTestSupport;
@@ -20,8 +21,10 @@
import org.cytoscape.io.internal.util.session.SessionUtil;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
@@ -44,6 +47,7 @@
CyNetworkViewFactory networkViewFactory;
CyNetworkFactory networkFactory;
CyRootNetworkManager rootNetworkMgr;
+ CyNetworkTableManager netTablMgr;
CyTableFactory tableFactory;
RenderingEngineManager renderingEngineMgr;
ReadDataManager readDataMgr;
@@ -67,11 +71,12 @@
NetworkTestSupport networkTestSupport = new
NetworkTestSupport();
networkFactory = networkTestSupport.getNetworkFactory();
rootNetworkMgr = networkTestSupport.getRootNetworkFactory();
+ netTablMgr = networkTestSupport.getNetworkTableManager();
NetworkViewTestSupport networkViewTestSupport = new
NetworkViewTestSupport();
networkViewFactory =
networkViewTestSupport.getNetworkViewFactory();
- readCache = new ReadCache();
+ readCache = new ReadCache(netTablMgr);
suidUpdater = new SUIDUpdater();
readDataMgr = new ReadDataManager(readCache, suidUpdater,
mock(EquationCompiler.class), networkFactory, rootNetworkMgr);
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