Author: mes
Date: 2010-08-10 14:41:02 -0700 (Tue, 10 Aug 2010)
New Revision: 21289
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/ssf/test/SSFReaderTest.java
Log:
changed how CyDataTables are managed for networks
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java
2010-08-10 20:31:28 UTC (rev 21288)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java
2010-08-10 21:41:02 UTC (rev 21289)
@@ -13,6 +13,7 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.GraphObject;
+import org.cytoscape.model.CyTableManager;
import org.cytoscape.session.CyNetworkManager;
import static org.cytoscape.model.GraphObject.*;
@@ -31,12 +32,14 @@
private String primaryKey = "name";
private CyNetworkManager manager;
+ private CyTableManager tableMgr;
- public TextDataTableReader(CyNetworkManager manager, String objType) {
+ public TextDataTableReader(CyNetworkManager manager, String objType,
CyTableManager tableMgr) {
super();
this.objectType = objType;
this.manager = manager;
delimiter = DEF_DELIMITER;
+ this.tableMgr = tableMgr;
}
public Map<Class<?>, Object> read() throws IOException {
@@ -45,7 +48,8 @@
if( network == null)
throw new IllegalStateException("Could not find current
network.");
- final Map<String, CyDataTable> tables =
network.getCyDataTables(objectType);
+ //final Map<String, CyDataTable> tables =
network.getCyDataTables(objectType);
+ final Map<String, CyDataTable> tables =
tableMgr.getTableMap(objectType, network);
final CyDataTable table = tables.get(CyNetwork.DEFAULT_ATTRS);
if( table == null)
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2010-08-10 20:31:28 UTC (rev 21288)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2010-08-10 21:41:02 UTC (rev 21289)
@@ -41,6 +41,7 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyDataTable;
+import org.cytoscape.model.CyTableManager;
//import org.cytoscape.groups.CyGroup;
//import cytoscape.groups.CyGroupManager;
//TODO
@@ -203,6 +204,7 @@
private Writer writer = null;
private boolean doFullEncoding;
+ private CyTableManager tableMgr;
/**
* Constructor.<br>
@@ -215,10 +217,11 @@
* @throws URISyntaxException
* @throws JAXBException
*/
- public XGMMLWriter(final CyNetwork network, final CyNetworkView view)
+ public XGMMLWriter(final CyNetwork network, final CyNetworkView view,
final CyTableManager tableMgr)
throws IOException, URISyntaxException {
this.network = network;
this.networkView = view;
+ this.tableMgr = tableMgr;
// groupList = new ArrayList<CyGroup>();
nodeMap = new HashMap<CyNode,CyNode>();
@@ -246,8 +249,8 @@
* @throws JAXBException
*/
public XGMMLWriter(final CyNetwork network, final CyNetworkView view,
- boolean noCytoscapeGraphics) throws IOException,
URISyntaxException {
- this(network, view);
+ boolean noCytoscapeGraphics, final CyTableManager
tm) throws IOException, URISyntaxException {
+ this(network, view, tm);
this.noCytoscapeGraphics = noCytoscapeGraphics;
}
@@ -410,7 +413,7 @@
// Now handle all of the other network attributes
// TODO this isn't *serializing* namespaces - I would expect
name clashes with this approach
- for ( CyDataTable table :
network.getNetworkCyDataTables().values() ) {
+ for ( CyDataTable table :
tableMgr.getTableMap("NETWORK",network).values() ) {
CyRow row = table.getRow(network.getSUID());
for ( String attName :
table.getColumnTypeMap().keySet() )
writeAttribute(row, attName);
Modified:
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-08-10 20:31:28 UTC (rev 21288)
+++
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-08-10 21:41:02 UTC (rev 21289)
@@ -7,16 +7,21 @@
<!-- Import services -->
- <osgi:reference id="cyLayoutsServiceRef"
interface="org.cytoscape.view.layout.CyLayouts" />
+ <osgi:reference id="cyLayoutsServiceRef"
+ interface="org.cytoscape.view.layout.CyLayouts" />
<osgi:reference id="cyNetworkFactoryServiceRef"
- interface="org.cytoscape.model.CyNetworkFactory" />
+ interface="org.cytoscape.model.CyNetworkFactory" />
<osgi:reference id="cyNetworkViewFactoryServiceRef"
- interface="org.cytoscape.view.model.CyNetworkViewFactory" />
+ interface="org.cytoscape.view.model.CyNetworkViewFactory" />
- <osgi:reference id="cyNetworkManagerServiceRef"
interface="org.cytoscape.session.CyNetworkManager" />
+ <osgi:reference id="cyNetworkManagerServiceRef"
+ interface="org.cytoscape.session.CyNetworkManager" />
+ <osgi:reference id="cyTableManagerServiceRef"
+ interface="org.cytoscape.model.CyTableManager" />
+
<!-- Export services -->
<osgi:service id="cyReaderManagerService" ref="cyReaderManager"
interface="org.cytoscape.io.read.CyReaderManager">
Modified:
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
--- core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2010-08-10 20:31:28 UTC (rev 21288)
+++ core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2010-08-10 21:41:02 UTC (rev 21289)
@@ -145,14 +145,17 @@
<bean id="nodeTextDataTableReader"
class="org.cytoscape.io.internal.read.datatable.TextDataTableReader">
<constructor-arg ref="cyNetworkManagerServiceRef" />
<constructor-arg value="NODE" />
+ <constructor-arg ref="cyTableManagerServiceRef" />
</bean>
<bean id="edgeTextDataTableReader"
class="org.cytoscape.io.internal.read.datatable.TextDataTableReader">
<constructor-arg ref="cyNetworkManagerServiceRef" />
<constructor-arg value="EDGE" />
+ <constructor-arg ref="cyTableManagerServiceRef" />
</bean>
<bean id="networkTextDataTableReader"
class="org.cytoscape.io.internal.read.datatable.TextDataTableReader">
<constructor-arg ref="cyNetworkManagerServiceRef" />
<constructor-arg value="NETWORK" />
+ <constructor-arg ref="cyTableManagerServiceRef" />
</bean>
<!-- Property Readers -->
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/ssf/test/SSFReaderTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/ssf/test/SSFReaderTest.java
2010-08-10 20:31:28 UTC (rev 21288)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/ssf/test/SSFReaderTest.java
2010-08-10 21:41:02 UTC (rev 21289)
@@ -11,6 +11,7 @@
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.io.internal.read.ssf.SSFReader;
import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyTableManager;
import org.cytoscape.model.internal.CyNetworkFactoryImpl;
import org.cytoscape.model.internal.CyRootNetworkFactoryImpl;
import org.cytoscape.model.subnetwork.CyRootNetwork;
@@ -28,6 +29,7 @@
private CyEventHelper helperMock;
private CyNetworkFactory factory;
private CyRootNetworkFactory rnFactory;
+ private CyTableManager tableMgr;
final File testFile1 = new File(FILE_LOCATION + "ssf_test1.ssf");
final File testFile2 = new File(FILE_LOCATION + "ssf_test2.ssf");
@@ -39,7 +41,8 @@
rnFactory = new CyRootNetworkFactoryImpl();
reader = new SSFReader(rnFactory);
helperMock = createMock(CyEventHelper.class);
- factory = new CyNetworkFactoryImpl(helperMock);
+ tableMgr = createMock(CyTableManager.class);
+ factory = new CyNetworkFactoryImpl(helperMock,tableMgr);
}
@After
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