Author: rozagh
Date: 2012-08-29 16:23:32 -0700 (Wed, 29 Aug 2012)
New Revision: 30291
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AbstractLoadAttributesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/CombineReaderAndMappingTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTaskFactoryImpl.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTaskFactoryImpl.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapTableToNetworkTablesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapTableToNetworkTablesTaskFactoryImpl.java
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTaskFactoryImplTest.java
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTaskFactoryImplTest.java
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/table/MapTableToNetworkTableTaskTest.java
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/table/MappingIntegrationTest.java
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/table/UpdateAddedNetworkAttributeTaskTest.java
Log:
fixes #1402 mapping the virtual columns to local tables of subnetworks for
selected only condition and to default attrs of root network for map to all
condition.
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -221,8 +221,8 @@
CyTableWriterManager cyTableWriterManagerRef =
getService(bc,CyTableWriterManager.class);
SynchronousTaskManager<?> synchronousTaskManagerServiceRef =
getService(bc,SynchronousTaskManager.class);
TunableSetter tunableSetterServiceRef =
getService(bc,TunableSetter.class);
+ CyRootNetworkManager rootNetworkManagerServiceRef =
getService(bc, CyRootNetworkManager.class);
-
CyGroupManager cyGroupManager = getService(bc,
CyGroupManager.class);
CyGroupFactory cyGroupFactory = getService(bc,
CyGroupFactory.class);
@@ -300,8 +300,8 @@
registerService(bc, updateAddedNetworkAttributes,
SessionLoadedListener.class, new Properties());
- LoadAttributesFileTaskFactoryImpl loadAttrsFileTaskFactory =
new LoadAttributesFileTaskFactoryImpl(cyDataTableReaderManagerServiceRef,
tunableSetterServiceRef,cyNetworkManagerServiceRef, cyTableManagerServiceRef,
updateAddedNetworkAttributes);
- LoadAttributesURLTaskFactoryImpl loadAttrsURLTaskFactory = new
LoadAttributesURLTaskFactoryImpl(cyDataTableReaderManagerServiceRef,
tunableSetterServiceRef, cyNetworkManagerServiceRef, cyTableManagerServiceRef,
updateAddedNetworkAttributes);
+ LoadAttributesFileTaskFactoryImpl loadAttrsFileTaskFactory =
new LoadAttributesFileTaskFactoryImpl(cyDataTableReaderManagerServiceRef,
tunableSetterServiceRef,cyNetworkManagerServiceRef, cyTableManagerServiceRef,
updateAddedNetworkAttributes,rootNetworkManagerServiceRef );
+ LoadAttributesURLTaskFactoryImpl loadAttrsURLTaskFactory = new
LoadAttributesURLTaskFactoryImpl(cyDataTableReaderManagerServiceRef,
tunableSetterServiceRef, cyNetworkManagerServiceRef, cyTableManagerServiceRef,
updateAddedNetworkAttributes, rootNetworkManagerServiceRef);
// Apply Visual Style Task
ApplyVisualStyleTaskFactoryimpl applyVisualStyleTaskFactory =
new ApplyVisualStyleTaskFactoryimpl(visualMappingManagerServiceRef);
@@ -1067,7 +1067,7 @@
// TODO: remove from group...
- MapTableToNetworkTablesTaskFactoryImpl mapNetworkToTables = new
MapTableToNetworkTablesTaskFactoryImpl(cyNetworkManagerServiceRef,
tunableSetterServiceRef, updateAddedNetworkAttributes);
+ MapTableToNetworkTablesTaskFactoryImpl mapNetworkToTables = new
MapTableToNetworkTablesTaskFactoryImpl(cyNetworkManagerServiceRef,
tunableSetterServiceRef, updateAddedNetworkAttributes,
rootNetworkManagerServiceRef);
Properties mapNetworkToTablesProps = new Properties();
registerService(bc, mapNetworkToTables,
MapTableToNetworkTablesTaskFactory.class, mapNetworkToTablesProps);
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -115,11 +115,12 @@
// create subnetwork and add selected nodes and appropriate
edges
final CySubNetwork newNet =
rootNetworkManager.getRootNetwork(parentNetwork).addSubNetwork();
+
+ //We need to cpy the columns to local tables, since copying
them to default table will duplicate the virtual columns.
+ addColumns(parentNetwork.getTable(CyNode.class,
CyNetwork.LOCAL_ATTRS), newNet.getTable(CyNode.class, CyNetwork.LOCAL_ATTRS));
+ addColumns(parentNetwork.getTable(CyEdge.class,
CyNetwork.LOCAL_ATTRS), newNet.getTable(CyEdge.class, CyNetwork.LOCAL_ATTRS) );
+ addColumns(parentNetwork.getTable(CyNetwork.class,
CyNetwork.LOCAL_ATTRS), newNet.getTable(CyNetwork.class,
CyNetwork.LOCAL_ATTRS));
- addColumns(parentNetwork.getDefaultNodeTable(),
newNet.getDefaultNodeTable() );
- addColumns(parentNetwork.getDefaultEdgeTable(),
newNet.getDefaultEdgeTable() );
- addColumns(parentNetwork.getDefaultNetworkTable(),
newNet.getDefaultNetworkTable());
-
tm.setProgress(0.3);
for (final CyNode node : selectedNodes){
@@ -174,13 +175,13 @@
VirtualColumnInfo colInfo = col.getVirtualColumnInfo();
CyColumn checkCol= subTable.getColumn(col.getName());
if(checkCol == null)
- subTable.addVirtualColumn(col.getName(),
colInfo.getSourceColumn(), colInfo.getSourceTable(),
colInfo.getTargetJoinKey(), true);
+ subTable.addVirtualColumn(col.getName(),
colInfo.getSourceColumn(), colInfo.getSourceTable(),
colInfo.getTargetJoinKey(), col.isImmutable());
else
if(!checkCol.getVirtualColumnInfo().isVirtual() ||
!checkCol.getVirtualColumnInfo().getSourceTable().equals(colInfo.getSourceTable())
||
!checkCol.getVirtualColumnInfo().getSourceColumn().equals(colInfo.getSourceColumn()))
- subTable.addVirtualColumn(col.getName(),
colInfo.getSourceColumn(), colInfo.getSourceTable(),
colInfo.getTargetJoinKey(), true);
+ subTable.addVirtualColumn(col.getName(),
colInfo.getSourceColumn(), colInfo.getSourceTable(),
colInfo.getTargetJoinKey(), col.isImmutable());
}
private void copyColumn(CyColumn col, CyTable subTable) {
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AbstractLoadAttributesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AbstractLoadAttributesTask.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AbstractLoadAttributesTask.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -7,6 +7,7 @@
import org.cytoscape.io.read.CyTableReaderManager;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.task.internal.table.MapTableToNetworkTablesTask;
import
org.cytoscape.task.internal.table.MapTableToNetworkTablesTaskFactoryImpl;
import org.cytoscape.task.internal.table.UpdateAddedNetworkAttributes;
@@ -22,13 +23,15 @@
private final CyNetworkManager netMgr;
private final CyTableManager tableMgr;
private final UpdateAddedNetworkAttributes updateAddedNetworkAttributes;
-
+ private final CyRootNetworkManager rootNetMgr;
+
public AbstractLoadAttributesTask(final CyTableReaderManager mgr, final
CyNetworkManager netMgr, final CyTableManager tabelMgr,
- final UpdateAddedNetworkAttributes
updateAddedNetworkAttributes) {
+ final UpdateAddedNetworkAttributes
updateAddedNetworkAttributes, final CyRootNetworkManager rootNetMgr) {
this.mgr = mgr;
this.netMgr = netMgr;
this.tableMgr = tabelMgr;
this.updateAddedNetworkAttributes =
updateAddedNetworkAttributes;
+ this.rootNetMgr = rootNetMgr;
}
void loadTable(final String name, final URI uri, final TaskMonitor
taskMonitor) throws Exception {
@@ -42,7 +45,7 @@
taskMonitor.setStatusMessage("Importing Data Table...");
- insertTasksAfterCurrentTask(new CombineReaderAndMappingTask(
reader, netMgr, updateAddedNetworkAttributes) , new
AddImportedTableTask(tableMgr, reader));
+ insertTasksAfterCurrentTask(new CombineReaderAndMappingTask(
reader, netMgr, updateAddedNetworkAttributes, rootNetMgr) , new
AddImportedTableTask(tableMgr, reader));
}
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/CombineReaderAndMappingTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/CombineReaderAndMappingTask.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/CombineReaderAndMappingTask.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -3,6 +3,7 @@
import org.cytoscape.io.read.CyTableReader;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTable;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.task.internal.table.MapTableToNetworkTablesTask;
import org.cytoscape.task.internal.table.UpdateAddedNetworkAttributes;
import org.cytoscape.work.AbstractTask;
@@ -27,9 +28,9 @@
public CyTableReader readerTask;
- public CombineReaderAndMappingTask(CyTableReader readerTask ,
CyNetworkManager networkManager, final UpdateAddedNetworkAttributes
updateAddedNetworkAttributes){
+ public CombineReaderAndMappingTask(CyTableReader readerTask ,
CyNetworkManager networkManager, final UpdateAddedNetworkAttributes
updateAddedNetworkAttributes, final CyRootNetworkManager rootNetMgr){
this.readerTask = readerTask;
- this.mappingTask = new
MapTableToNetworkTablesTask(networkManager, readerTask,
updateAddedNetworkAttributes);
+ this.mappingTask = new
MapTableToNetworkTablesTask(networkManager, readerTask,
updateAddedNetworkAttributes, rootNetMgr);
}
@Override
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTask.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTask.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -6,6 +6,7 @@
import org.cytoscape.io.read.CyTableReaderManager;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.task.internal.table.UpdateAddedNetworkAttributes;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
@@ -15,8 +16,9 @@
@Tunable(description="Attribute Table file",
params="fileCategory=table;input=true")
public File file;
- public LoadAttributesFileTask(final CyTableReaderManager mgr, final
CyNetworkManager netMgr, final CyTableManager tabelMgr, final
UpdateAddedNetworkAttributes updateAddedNetworkAttributes) {
- super(mgr, netMgr, tabelMgr, updateAddedNetworkAttributes);
+ public LoadAttributesFileTask(final CyTableReaderManager mgr, final
CyNetworkManager netMgr, final CyTableManager tabelMgr,
+ final UpdateAddedNetworkAttributes
updateAddedNetworkAttributes, final CyRootNetworkManager rootNetMgr) {
+ super(mgr, netMgr, tabelMgr, updateAddedNetworkAttributes,
rootNetMgr);
}
/**
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTaskFactoryImpl.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTaskFactoryImpl.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -8,6 +8,7 @@
import org.cytoscape.io.read.CyTableReaderManager;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.task.internal.table.UpdateAddedNetworkAttributes;
import org.cytoscape.task.read.LoadTableFileTaskFactory;
import org.cytoscape.work.AbstractTaskFactory;
@@ -22,18 +23,20 @@
private final CyNetworkManager netMgr;
private final CyTableManager tableMgr;
private final UpdateAddedNetworkAttributes updateAddedNetworkAttributes;
+ private final CyRootNetworkManager rootNetMgr;
public LoadAttributesFileTaskFactoryImpl(CyTableReaderManager mgr,
TunableSetter tunableSetter, final CyNetworkManager netMgr,
- final CyTableManager tabelMgr, final
UpdateAddedNetworkAttributes updateAddedNetworkAttributes) {
+ final CyTableManager tabelMgr, final
UpdateAddedNetworkAttributes updateAddedNetworkAttributes, final
CyRootNetworkManager rootNetMgr) {
this.mgr = mgr;
this.tunableSetter = tunableSetter;
this.netMgr = netMgr;
this.tableMgr = tabelMgr;
this.updateAddedNetworkAttributes =
updateAddedNetworkAttributes;
+ this.rootNetMgr = rootNetMgr;
}
public TaskIterator createTaskIterator() {
- return new TaskIterator(2, new LoadAttributesFileTask(mgr,
netMgr, tableMgr, updateAddedNetworkAttributes));
+ return new TaskIterator(2, new LoadAttributesFileTask(mgr,
netMgr, tableMgr, updateAddedNetworkAttributes, rootNetMgr));
}
@Override
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTask.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTask.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -6,6 +6,7 @@
import org.cytoscape.io.read.CyTableReaderManager;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.task.internal.table.UpdateAddedNetworkAttributes;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
@@ -16,8 +17,9 @@
@Tunable(description="Attribute Table URL",
params="fileCategory=table;input=true")
public URL url;
- public LoadAttributesURLTask(final CyTableReaderManager mgr, final
CyNetworkManager netMgr, final CyTableManager tableMgr, final
UpdateAddedNetworkAttributes updateAddedNetworkAttributes) {
- super(mgr, netMgr, tableMgr, updateAddedNetworkAttributes);
+ public LoadAttributesURLTask(final CyTableReaderManager mgr, final
CyNetworkManager netMgr, final CyTableManager tableMgr,
+ final UpdateAddedNetworkAttributes
updateAddedNetworkAttributes, final CyRootNetworkManager rootNetMgr) {
+ super(mgr, netMgr, tableMgr, updateAddedNetworkAttributes,
rootNetMgr);
}
/**
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTaskFactoryImpl.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTaskFactoryImpl.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -8,6 +8,7 @@
import org.cytoscape.io.read.CyTableReaderManager;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.task.internal.table.UpdateAddedNetworkAttributes;
import org.cytoscape.task.read.LoadTableFileTaskFactory;
import org.cytoscape.task.read.LoadTableURLTaskFactory;
@@ -24,17 +25,20 @@
private final CyNetworkManager netMgr;
private final CyTableManager tableMgr;
private final UpdateAddedNetworkAttributes
updateAddedNetworkAttributes;
+ private final CyRootNetworkManager rootNetMgr;
+
public LoadAttributesURLTaskFactoryImpl(CyTableReaderManager mgr,
TunableSetter tunableSetter, final CyNetworkManager netMgr,
- final CyTableManager tabelMgr, final
UpdateAddedNetworkAttributes updateAddedNetworkAttributes) {
+ final CyTableManager tabelMgr, final
UpdateAddedNetworkAttributes updateAddedNetworkAttributes, final
CyRootNetworkManager rootNetMgr) {
this.mgr = mgr;
this.tunableSetter = tunableSetter;
this.netMgr = netMgr;
this.tableMgr = tabelMgr;
this.updateAddedNetworkAttributes =
updateAddedNetworkAttributes;
+ this.rootNetMgr = rootNetMgr;
}
public TaskIterator createTaskIterator() {
- return new TaskIterator(2, new LoadAttributesURLTask(mgr,
netMgr, tableMgr, updateAddedNetworkAttributes));
+ return new TaskIterator(2, new LoadAttributesURLTask(mgr,
netMgr, tableMgr, updateAddedNetworkAttributes, rootNetMgr));
}
@Override
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapTableToNetworkTablesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapTableToNetworkTablesTask.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapTableToNetworkTablesTask.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -13,6 +13,8 @@
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.ProvidesTitle;
import org.cytoscape.work.TaskMonitor;
@@ -23,45 +25,46 @@
import org.slf4j.LoggerFactory;
public final class MapTableToNetworkTablesTask extends AbstractTask {
-
+
enum TableType {
NODE_ATTR("Node Attributes", CyNode.class), EDGE_ATTR("Edge
Attributes", CyEdge.class), NETWORK_ATTR("Network Attributes",
CyNetwork.class), GLOBAL("Unassigned Tables", CyTable.class);
private final String name;
private final Class<? extends CyIdentifiable> type;
-
+
private TableType(final String name, Class<? extends
CyIdentifiable> type) {
this.name = name;
this.type = type;
}
-
+
public Class<? extends CyIdentifiable> getType(){
return this.type;
}
-
+
@Override
public String toString() {
return name;
}
};
-
+
private static Logger logger =
LoggerFactory.getLogger(MapTableToNetworkTablesTask.class);
private static String NO_NETWORKS = "No Networks Found";
private final CyNetworkManager networkManager;
+ private final CyRootNetworkManager rootNetworkManager;
private final CyTable globalTable;
private final CyTableReader reader;
private final boolean byReader;
private Map<String, CyNetwork> name2NetworkMap;
private final UpdateAddedNetworkAttributes updateAddedNetworkAttributes;
-
-
+
+
@Tunable(description = "Import Data To:")
public ListSingleSelection<TableType> dataTypeOptions;
-
+
//******* we couldnt use the enum to check the dependency. So, update
this line if you change the GLOBAL enum string
@Tunable(description = "Apply to Selected Networks
Only",groups="Network Options", dependsOn="dataTypeOptions!=Unassigned Tables",
params="displayState=collapsed")
public boolean selectedNetworksOnly = false;
-
+
@Tunable(description = "Network List",groups="Network
Options",dependsOn="selectedNetworksOnly=true", params="displayState=collapsed")
public ListMultipleSelection<String> networkList;
@@ -71,36 +74,39 @@
return "Import Data ";
}
-
- public MapTableToNetworkTablesTask(final CyNetworkManager
networkManager, final CyTableReader reader, final UpdateAddedNetworkAttributes
updateAddedNetworkAttributes){
+
+ public MapTableToNetworkTablesTask(final CyNetworkManager
networkManager, final CyTableReader reader, final UpdateAddedNetworkAttributes
updateAddedNetworkAttributes, final CyRootNetworkManager rootNetworkManager ){
this.reader = reader;
globalTable = null;
this.byReader = true;
this.networkManager = networkManager;
this.name2NetworkMap = new HashMap<String, CyNetwork>();
this.updateAddedNetworkAttributes =
updateAddedNetworkAttributes;
-
+ this.rootNetworkManager = rootNetworkManager;
+
initTunable(networkManager);
-
+
}
-
- public MapTableToNetworkTablesTask(final CyNetworkManager
networkManager, final CyTable globalTable, final UpdateAddedNetworkAttributes
updateAddedNetworkAttributes){
+
+ public MapTableToNetworkTablesTask(final CyNetworkManager
networkManager, final CyTable globalTable, final UpdateAddedNetworkAttributes
updateAddedNetworkAttributes, final CyRootNetworkManager rootNetworkManager){
this.networkManager = networkManager;
this.globalTable = globalTable;
this.byReader = false;
this.reader = null;
this.name2NetworkMap = new HashMap<String, CyNetwork>();
this.updateAddedNetworkAttributes =
updateAddedNetworkAttributes;
+ this.rootNetworkManager = rootNetworkManager;
+
initTunable(networkManager);
}
-
+
private void initTunable(CyNetworkManager networkManage){
final List<TableType> options = new ArrayList<TableType>();
for(TableType type: TableType.values())
options.add(type);
dataTypeOptions = new ListSingleSelection<TableType>(options);
dataTypeOptions.setSelectedValue(TableType.NODE_ATTR);
-
+
for(CyNetwork net: networkManage.getNetworkSet()){
String netName = net.getRow(net).get(CyNetwork.NAME,
String.class);
name2NetworkMap.put(netName, net);
@@ -111,35 +117,23 @@
networkList = new
ListMultipleSelection<String>(NO_NETWORKS);
else
networkList = new ListMultipleSelection<String>(names);
-
+
}
-
-
+
+
public void run(TaskMonitor taskMonitor) throws Exception {
TableType tableType = dataTypeOptions.getSelectedValue();
- if (tableType != TableType.GLOBAL ){
- List<CyNetwork> networks = new ArrayList<CyNetwork>();
+ if (tableType == TableType.GLOBAL )
+ return;
- if (!selectedNetworksOnly)
- networks.addAll(networkManager.getNetworkSet());
- else{
-
if(!networkList.getSelectedValues().get(0).equals(NO_NETWORKS))
- for(String netName:
networkList.getSelectedValues())
-
networks.add(name2NetworkMap.get(netName));
+ List<CyNetwork> networks = new ArrayList<CyNetwork>();
- }
- for (CyNetwork network: networks){
- CyTable targetTable = getTable(network,
tableType);
- if (targetTable != null){
- if(byReader){
- if (reader.getTables() != null
&& reader.getTables().length >0){
- for(CyTable sourceTable
: reader.getTables())
-
mapTable(targetTable, sourceTable);
- }
- }else
- mapTable(targetTable,
globalTable);
- }
- }
+ if (!selectedNetworksOnly)
+ mapTableToDefaultAttrs (tableType);
+ else
+ mapTableToLocalAttrs (tableType);
+
+
if(!selectedNetworksOnly){ //if table should be mapped
to all of the tables
//add each mapped table to the list for mapping
to networks going to be added later
if(byReader){
@@ -148,23 +142,67 @@
updateAddedNetworkAttributes.addMappingToList(sourceTable, tableType.getType());
}else
updateAddedNetworkAttributes.addMappingToList(globalTable, tableType.getType());
+
}
+
+ }
+
+
+
+ private void mapTableToLocalAttrs(TableType tableType) {
+ List<CyNetwork> networks = new ArrayList<CyNetwork>();
+
+ if(!networkList.getSelectedValues().get(0).equals(NO_NETWORKS))
+ for(String netName: networkList.getSelectedValues())
+ networks.add(name2NetworkMap.get(netName));
+
+ for (CyNetwork network: networks){
+ CyTable targetTable = getTable(network, tableType,
CyNetwork.LOCAL_ATTRS);
+ if (targetTable != null)
+ applyMapping(targetTable);
}
+
}
+ private void mapTableToDefaultAttrs(TableType tableType) {
+ List<CyRootNetwork> rootNetworkList = new
ArrayList<CyRootNetwork>();
+ for (CyNetwork net : networkManager.getNetworkSet())
+ if (!
rootNetworkList.contains(rootNetworkManager.getRootNetwork(net)))
+ rootNetworkList.add(
rootNetworkManager.getRootNetwork(net));
- private CyTable getTable(CyNetwork network, TableType tableType){
+ for (CyRootNetwork root: rootNetworkList ){
+ CyTable targetTable = getTable(root, tableType,
CyNetwork.DEFAULT_ATTRS);
+ if (targetTable != null){
+ applyMapping(targetTable);
+ }
+ }
+ }
+
+
+ private CyTable getTable(CyNetwork network, TableType tableType, String
namespace){
if (tableType == TableType.NODE_ATTR)
- return network.getDefaultNodeTable();
+ return network.getTable(CyNode.class, namespace);
if (tableType == TableType.EDGE_ATTR)
- return network.getDefaultEdgeTable();
+ return network.getTable(CyEdge.class, namespace);
if (tableType == TableType.NETWORK_ATTR)
- return network.getDefaultNetworkTable();
+ return network.getTable(CyNetwork.class, namespace);
+
logger.warn("The selected table type is not valie. \nTable
needs to be one of these types: " +TableType.NODE_ATTR +", " +
TableType.EDGE_ATTR + ", "+ TableType.NETWORK_ATTR +" or "+TableType.GLOBAL
+".");
return null;
}
-
+
+
+ private void applyMapping(CyTable targetTable){
+ if(byReader){
+ if (reader.getTables() != null &&
reader.getTables().length >0){
+ for(CyTable sourceTable : reader.getTables())
+ mapTable(targetTable, sourceTable);
+ }
+ }else
+ mapTable(targetTable, globalTable);
+ }
+
private void mapTable(final CyTable localTable, final CyTable
globalTable) {
if (globalTable.getPrimaryKey().getType() != String.class)
throw new IllegalStateException("Local table's primary
key should be type String.");
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapTableToNetworkTablesTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapTableToNetworkTablesTaskFactoryImpl.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/table/MapTableToNetworkTablesTaskFactoryImpl.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -9,6 +9,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTable;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.task.AbstractTableTaskFactory;
import org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory;
import org.cytoscape.task.internal.table.MapTableToNetworkTablesTask.TableType;
@@ -23,17 +24,19 @@
private final CyNetworkManager networkManager;
private final TunableSetter tunableSetter;
private final UpdateAddedNetworkAttributes updateAddedNetworkAttributes;
+ private final CyRootNetworkManager rootNetMgr;
- public MapTableToNetworkTablesTaskFactoryImpl( final CyNetworkManager
networkManager, final TunableSetter tunableSetter, final
UpdateAddedNetworkAttributes updateAddedNetworkAttributes ){
+ public MapTableToNetworkTablesTaskFactoryImpl( final CyNetworkManager
networkManager, final TunableSetter tunableSetter, final
UpdateAddedNetworkAttributes updateAddedNetworkAttributes, final
CyRootNetworkManager rootNetMgr ){
this.networkManager = networkManager;
this.tunableSetter = tunableSetter;
this.updateAddedNetworkAttributes =
updateAddedNetworkAttributes;
+ this.rootNetMgr = rootNetMgr;
}
@Override
public TaskIterator createTaskIterator(CyTable globalTable) {
- return new TaskIterator(new
MapTableToNetworkTablesTask(networkManager, globalTable,
updateAddedNetworkAttributes));
+ return new TaskIterator(new
MapTableToNetworkTablesTask(networkManager, globalTable,
updateAddedNetworkAttributes, rootNetMgr));
}
@Override
Modified:
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTaskFactoryImplTest.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTaskFactoryImplTest.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTaskFactoryImplTest.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -10,6 +10,7 @@
import org.cytoscape.io.read.CyTableReaderManager;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.task.internal.table.UpdateAddedNetworkAttributes;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskIterator;
@@ -38,6 +39,9 @@
@Mock
UpdateAddedNetworkAttributes updateAddedNetworkAttributes;
+ @Mock
+ CyRootNetworkManager rootNetMgr;
+
@Before
public void initMocks() {
MockitoAnnotations.initMocks(this);
@@ -47,7 +51,7 @@
@Test(expected = NullPointerException.class)
public void testLoadAttributesFileTaskFactory() throws Exception {
- final LoadAttributesFileTaskFactoryImpl factory = new
LoadAttributesFileTaskFactoryImpl(rmgr, ts, netMgr, tabMgr,
updateAddedNetworkAttributes);
+ final LoadAttributesFileTaskFactoryImpl factory = new
LoadAttributesFileTaskFactoryImpl(rmgr, ts, netMgr, tabMgr,
updateAddedNetworkAttributes, rootNetMgr);
TaskIterator ti = factory.createTaskIterator();
assertNotNull(ti);
Modified:
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTaskFactoryImplTest.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTaskFactoryImplTest.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTaskFactoryImplTest.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -9,6 +9,7 @@
import org.cytoscape.io.read.CyTableReaderManager;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.task.internal.table.UpdateAddedNetworkAttributes;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskIterator;
@@ -39,6 +40,9 @@
@Mock
UpdateAddedNetworkAttributes updateAddedNetworkAttributes;
+ @Mock
+ CyRootNetworkManager rootNetMgr;
+
@Before
public void initMocks() {
MockitoAnnotations.initMocks(this);
@@ -48,7 +52,7 @@
@Test(expected = NullPointerException.class)
public void testLoadAttributesURLTaskFactory() throws Exception {
- final LoadAttributesURLTaskFactoryImpl factory = new
LoadAttributesURLTaskFactoryImpl(rmgr, ts, netMgr, tabMgr,
updateAddedNetworkAttributes);
+ final LoadAttributesURLTaskFactoryImpl factory = new
LoadAttributesURLTaskFactoryImpl(rmgr, ts, netMgr, tabMgr,
updateAddedNetworkAttributes, rootNetMgr);
final TaskIterator ti = factory.createTaskIterator();
assertNotNull(ti);
Modified:
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/table/MapTableToNetworkTableTaskTest.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/table/MapTableToNetworkTableTaskTest.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/table/MapTableToNetworkTableTaskTest.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -16,11 +16,11 @@
import org.cytoscape.model.NetworkTestSupport;
import org.cytoscape.model.SavePolicy;
import org.cytoscape.model.internal.CyNetworkManagerImpl;
+import org.cytoscape.model.internal.CyRootNetworkManagerImpl;
import org.cytoscape.model.internal.CyTableImpl;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.TunableHandlerFactory;
import org.junit.Test;
import static org.mockito.Mockito.mock;
@@ -48,6 +48,8 @@
private static CyEventHelper eventHelper = new DummyCyEventHelper();
private static CyNetworkManagerImpl netMgr = new
CyNetworkManagerImpl(eventHelper);
+ private static CyRootNetworkManagerImpl rootNetMgr = new
CyRootNetworkManagerImpl();
+
private static SyncTunableMutator stm = new SyncTunableMutator();
private static SyncTunableHandlerFactory syncTunableHandlerFactory =
new SyncTunableHandlerFactory();
private static TunableSetterImpl ts =new TunableSetterImpl(new
SyncTunableMutatorFactory(syncTunableHandlerFactory), new
TunableRecorderManager());
@@ -88,7 +90,7 @@
public static void mapping(CyTable table, CyNetwork net, boolean
selectedOnly) throws Exception{
UpdateAddedNetworkAttributes up = new
UpdateAddedNetworkAttributes(new
MapGlobalToLocalTableTaskFactoryImpl(mock(CyTableManager.class), netMgr, ts),
new SyncTaskManager(stm));
- MapTableToNetworkTablesTaskFactoryImpl mappingTF = new
MapTableToNetworkTablesTaskFactoryImpl(netMgr, ts, up);
+ MapTableToNetworkTablesTaskFactoryImpl mappingTF = new
MapTableToNetworkTablesTaskFactoryImpl(netMgr, ts, up , rootNetMgr);
List<CyNetwork> nets = new ArrayList<CyNetwork>();
nets.add(net);
Modified:
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/table/MappingIntegrationTest.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/table/MappingIntegrationTest.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/table/MappingIntegrationTest.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -26,9 +26,11 @@
import org.cytoscape.model.events.NetworkAddedEvent;
import org.cytoscape.model.internal.CyNetworkManagerImpl;
import org.cytoscape.model.internal.CyNetworkTableManagerImpl;
+import org.cytoscape.model.internal.CyRootNetworkManagerImpl;
import org.cytoscape.model.internal.CySubNetworkImpl;
import org.cytoscape.model.internal.CyTableImpl;
import org.cytoscape.model.internal.CyTableManagerImpl;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.task.internal.creation.NewNetworkSelectedNodesOnlyTask;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -56,6 +58,8 @@
private CyEventHelper eventHelper = new DummyCyEventHelper();
private CyNetworkManagerImpl netMgr = new
CyNetworkManagerImpl(eventHelper);
+ private final CyRootNetworkManagerImpl rootNetMgr = new
CyRootNetworkManagerImpl();
+
private SyncTunableMutator stm = new SyncTunableMutator();
SyncTunableHandlerFactory syncTunableHandlerFactory = new
SyncTunableHandlerFactory();
@@ -142,6 +146,7 @@
((CySubNetworkImpl) subnet1).handleEvent(new
NetworkAddedEvent(netMgr, subnet1));
+
assertEquals(2, subnet1.getNodeList().size());
assertNotNull(subnet1.getDefaultNodeTable().getColumn(table1sCol));
@@ -163,8 +168,8 @@
//check the mapping by task
assertNotNull(net1.getDefaultNodeTable().getColumn(table2sCol));
assertEquals(table2sRow1,
net1.getDefaultNodeTable().getRow(node1.getSUID()).get(table2sCol,
String.class) );
- // TODO!!!
-
//assertNull(subnet1.getDefaultNodeTable().getColumn(table2sCol)); //subnet1
should not be mapped
+
+
assertNull(subnet1.getDefaultNodeTable().getColumn(table2sCol)); //subnet1
should not be mapped
//creating another subnetwork (subnet2) to check that bot
virtual columns will be added
net1.getDefaultNodeTable().getRow(node1.getSUID()).set(CyNetwork.SELECTED,
true);
@@ -201,7 +206,7 @@
public void mapping(CyTable table, CyNetwork net, boolean selectedOnly)
throws Exception{
- MapTableToNetworkTablesTaskFactoryImpl mappingTF = new
MapTableToNetworkTablesTaskFactoryImpl(netMgr, ts, up);
+ MapTableToNetworkTablesTaskFactoryImpl mappingTF = new
MapTableToNetworkTablesTaskFactoryImpl(netMgr, ts, up, rootNetMgr);
List<CyNetwork> nets = new ArrayList<CyNetwork>();
nets.add(net);
Modified:
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/table/UpdateAddedNetworkAttributeTaskTest.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/table/UpdateAddedNetworkAttributeTaskTest.java
2012-08-29 21:54:33 UTC (rev 30290)
+++
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/table/UpdateAddedNetworkAttributeTaskTest.java
2012-08-29 23:23:32 UTC (rev 30291)
@@ -22,6 +22,7 @@
import org.cytoscape.model.events.NetworkAddedEvent;
import org.cytoscape.model.internal.CyNetworkManagerImpl;
import org.cytoscape.model.internal.CyNetworkTableManagerImpl;
+import org.cytoscape.model.internal.CyRootNetworkManagerImpl;
import org.cytoscape.model.internal.CySubNetworkImpl;
import org.cytoscape.model.internal.CyTableImpl;
import org.cytoscape.model.internal.CyTableManagerImpl;
@@ -47,7 +48,9 @@
private CyEventHelper eventHelper = new DummyCyEventHelper();
- private CyNetworkManagerImpl netMgr = new
CyNetworkManagerImpl(eventHelper);
+ private CyNetworkManagerImpl netMgr = new
CyNetworkManagerImpl(eventHelper);
+ private CyRootNetworkManagerImpl rootNetMgr = new
CyRootNetworkManagerImpl();
+
private SyncTunableMutator stm = new SyncTunableMutator();
SyncTunableHandlerFactory syncTunableHandlerFactory = new
SyncTunableHandlerFactory();
private TunableSetterImpl ts = new TunableSetterImpl(new
SyncTunableMutatorFactory(syncTunableHandlerFactory), new
TunableRecorderManager());
@@ -172,7 +175,7 @@
public void mapping(CyTable table, CyNetwork net, boolean selectedOnly
) throws Exception{
- MapTableToNetworkTablesTaskFactoryImpl mappingTF = new
MapTableToNetworkTablesTaskFactoryImpl(netMgr, ts, up);
+ MapTableToNetworkTablesTaskFactoryImpl mappingTF = new
MapTableToNetworkTablesTaskFactoryImpl(netMgr, ts, up, rootNetMgr);
List<CyNetwork> nets = new ArrayList<CyNetwork>();
nets.add(net);
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