Author: clopes
Date: 2012-04-03 13:24:20 -0700 (Tue, 03 Apr 2012)
New Revision: 28730
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportOntologyAndAnnotationTask.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
Log:
Fixes #843 : Global Table Browser registeres non-global tables to the combobox:
- CSV table reader no longer registers the tables it creates
- session manager registers all tables, including network ones
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
2012-04-03 19:34:03 UTC (rev 28729)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
2012-04-03 20:24:20 UTC (rev 28730)
@@ -187,7 +187,7 @@
XGMMLParser xgmmlParser = new
XGMMLParser(handlerFactory,readDataManager);
XGMMLNetworkReaderFactory xgmmlNetworkReaderFactory = new
XGMMLNetworkReaderFactory(xgmmlFilter,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,cyRootNetworkManagerServiceRef,renderingEngineManagerServiceRef,readDataManager,xgmmlParser,unrecognizedVisualPropertyManager);
XGMMLNetworkViewReaderFactory xgmmlNetworkViewReaderFactory =
new
XGMMLNetworkViewReaderFactory(xgmmlViewFilter,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,renderingEngineManagerServiceRef,readDataManager,xgmmlParser,unrecognizedVisualPropertyManager);
- CSVCyReaderFactory sessionTableReaderFactory = new
CSVCyReaderFactory(sessionTableFilter,true,true,cyTableFactoryServiceRef,compilerServiceRef,cyTableManagerServiceRef);
+ CSVCyReaderFactory sessionTableReaderFactory = new
CSVCyReaderFactory(sessionTableFilter,true,true,cyTableFactoryServiceRef,compilerServiceRef);
Cy3SessionReaderFactoryImpl cy3SessionReaderFactory = new
Cy3SessionReaderFactoryImpl(cys3Filter,readCache,cyNetworkReaderManager,cyPropertyReaderManager,vizmapReaderManager,sessionTableReaderFactory,cyNetworkTableManagerServiceRef,cyRootNetworkManagerServiceRef);
Cy2SessionReaderFactoryImpl cy2SessionReaderFactory = new
Cy2SessionReaderFactoryImpl(cys2Filter,readCache,cyNetworkReaderManager,cyPropertyReaderManager,vizmapReaderManager,cyRootNetworkManagerServiceRef);
CysessionReaderFactory cysessionReaderFactory = new
CysessionReaderFactory(cysessionFilter);
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
2012-04-03 19:34:03 UTC (rev 28729)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
2012-04-03 20:24:20 UTC (rev 28730)
@@ -18,7 +18,6 @@
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableFactory;
-import org.cytoscape.model.CyTableManager;
import org.cytoscape.work.TaskMonitor;
import au.com.bytecode.opencsv.CSVReader;
@@ -32,21 +31,19 @@
private final boolean handleEquations;
private final CyTableFactory tableFactory;
private final EquationCompiler compiler;
- private final CyTableManager tableManager;
private boolean isCanceled;
private CyTable table;
public CSVCyReader(final InputStream stream, final boolean readSchema,
final boolean handleEquations, final CyTableFactory
tableFactory,
- final EquationCompiler compiler, final
CyTableManager tableManager)
+ final EquationCompiler compiler)
{
this.stream = stream;
this.readSchema = readSchema;
this.handleEquations = handleEquations;
this.tableFactory = tableFactory;
this.compiler = compiler;
- this.tableManager = tableManager;
}
@Override
@@ -63,9 +60,6 @@
TableInfo info = readHeader(reader);
table = createTable(reader, info);
- taskMonitor.setProgress(0.6);
-
- tableManager.addTable(table);
taskMonitor.setProgress(1.0);
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
2012-04-03 19:34:03 UTC (rev 28729)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
2012-04-03 20:24:20 UTC (rev 28730)
@@ -7,7 +7,6 @@
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyTableFactory;
-import org.cytoscape.model.CyTableManager;
import org.cytoscape.work.TaskIterator;
@@ -16,23 +15,20 @@
private final boolean handleEquations;
private final CyTableFactory tableFactory;
private final EquationCompiler compiler;
- private final CyTableManager tableManager;
public CSVCyReaderFactory(final CyFileFilter filter, final boolean
readSchema,
final boolean handleEquations, final
CyTableFactory tableFactory,
- final EquationCompiler compiler, final
CyTableManager tableManager)
+ final EquationCompiler compiler)
{
super(filter);
this.readSchema = readSchema;
this.handleEquations = handleEquations;
this.tableFactory = tableFactory;
this.compiler = compiler;
- this.tableManager = tableManager;
}
@Override
public TaskIterator createTaskIterator(InputStream stream, String
inputName) {
- return new TaskIterator(new CSVCyReader(stream, readSchema,
handleEquations,
- tableFactory, compiler,
tableManager));
+ return new TaskIterator(new CSVCyReader(stream, readSchema,
handleEquations, tableFactory, compiler));
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
2012-04-03 19:34:03 UTC (rev 28729)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
2012-04-03 20:24:20 UTC (rev 28730)
@@ -451,15 +451,19 @@
}
private void mergeNetworkTables() throws UnsupportedEncodingException {
- for (Entry<Long, CyNetwork> entry : networkLookup.entrySet()) {
- CyNetwork network = entry.getValue();
- Object oldId = cache.getOldId(network.getSUID());
- Set<CyTableMetadataBuilder> builders =
networkTableMap.get(oldId);
+ for (Entry<Long, Set<CyTableMetadataBuilder>> entry :
networkTableMap.entrySet()) {
+ final Object oldId = entry.getKey();
+ final Set<CyTableMetadataBuilder> builders =
entry.getValue();
+ final CyNetwork network = cache.getNetwork(oldId);
- if (builders == null)
- continue;
+ if (network == null)
+ throw new RuntimeException("Cannot merge
network tables: Cannot find network " + oldId);
for (CyTableMetadataBuilder builder : builders) {
+ if ("VIEW".equals(builder.getNamespace())) {
+ continue; // TODO: disabled due to
timing conflicts with Ding (The VIEW tables are not created yet).
+ }
+
builder.setNetwork(network);
mergeNetworkTable(network, builder);
CyTableMetadata metadata = builder.build();
@@ -476,14 +480,10 @@
private void mergeNetworkTable(CyNetwork network,
CyTableMetadataBuilder builder) {
Class<? extends CyIdentifiable> type = (Class<? extends
CyIdentifiable>) builder.getType();
String namespace = builder.getNamespace();
-
- if ("VIEW".equals(namespace)) {
- return; // TODO: disabled due to timing conflicts with
Ding (The VIEW tables are not created yet).
- }
-
Map<String, CyTable> tableMap =
networkTableMgr.getTables(network, type);
CyTable targetTable = tableMap.get(namespace);
CyTable sourceTable = builder.getTable();
+
mergeTables(sourceTable, targetTable, type);
builder.setCyTable(targetTable);
}
Modified:
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
2012-04-03 19:34:03 UTC (rev 28729)
+++
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderTest.java
2012-04-03 20:24:20 UTC (rev 28730)
@@ -10,10 +10,9 @@
import java.io.UnsupportedEncodingException;
import java.util.List;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableManager;
-import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyTable.Mutability;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.TableTestSupport;
@@ -26,7 +25,6 @@
public class CSVCyReaderTest {
@Mock TaskMonitor taskMonitor;
- @Mock CyTableManager tableManager;
private CyTableFactory tableFactory;
@@ -45,8 +43,7 @@
public void testReadSimple() throws Exception {
String data = "SUID\r\njava.lang.Long\r\ntest
table,\"public\\,mutable\"\r\n5\r\n6";
CSVCyReader reader = new CSVCyReader(createStream(data), true,
- /* handleEquations = */
false, tableFactory,
- null, tableManager);
+ /* handleEquations = */
false, tableFactory, null);
reader.run(taskMonitor);
CyTable[] tables = reader.getTables();
assertNotNull(tables);
@@ -67,8 +64,7 @@
public void testReadString() throws Exception {
String data =
"SUID,name\r\njava.lang.Long,java.lang.String\r\ntest
table,\"public\\,mutable\"\r\n1,Alice\r\n2,Bob\r\n3,Carol";
CSVCyReader reader = new CSVCyReader(createStream(data), true,
- /* handleEquations = */
false, tableFactory,
- null, tableManager);
+ /* handleEquations = */
false, tableFactory, null);
reader.run(taskMonitor);
CyTable[] tables = reader.getTables();
CyTable table = tables[0];
@@ -80,8 +76,7 @@
public void testReadDouble() throws Exception {
String data =
"SUID,weight\r\njava.lang.Long,java.lang.Double\r\ntest
table,\"public\\,mutable\"\r\n0,0.56\r\n-5,-1.234";
CSVCyReader reader = new CSVCyReader(createStream(data), true,
- /* handleEquations = */
false, tableFactory,
- null, tableManager);
+ /* handleEquations = */
false, tableFactory, null);
reader.run(taskMonitor);
CyTable[] tables = reader.getTables();
CyTable table = tables[0];
@@ -93,8 +88,7 @@
public void testReadBoolean() throws Exception {
String data =
"SUID,hidden\r\njava.lang.Long,java.lang.Boolean\r\ntest
table,\"public\\,mutable\"\r\n30,true\r\n40,false\r\n50,true";
CSVCyReader reader = new CSVCyReader(createStream(data), true,
- /* handleEquations = */
false, tableFactory,
- null, tableManager);
+ /* handleEquations = */
false, tableFactory, null);
reader.run(taskMonitor);
CyTable[] tables = reader.getTables();
CyTable table = tables[0];
@@ -106,8 +100,7 @@
public void testReadList() throws Exception {
String data =
"SUID,list\r\njava.lang.Long,java.util.List<java.lang.String>\r\ntest
table,\"public\\,mutable\"\r\n1,\"a\rb\rc\"";
CSVCyReader reader = new CSVCyReader(createStream(data), true,
- /* handleEquations = */
false, tableFactory,
- null, tableManager);
+ /* handleEquations = */
false, tableFactory, null);
reader.run(taskMonitor);
CyTable[] tables = reader.getTables();
CyTable table = tables[0];
Modified:
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
===================================================================
---
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
2012-04-03 19:34:03 UTC (rev 28729)
+++
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
2012-04-03 20:24:20 UTC (rev 28730)
@@ -262,12 +262,12 @@
}
private void restoreTables(CySession sess) {
- // Register global tables
+ // Register all tables, if not already registered
for (CyTableMetadata metadata : sess.getTables()) {
- CyNetwork network = metadata.getNetwork();
+ final CyTable tbl = metadata.getTable();
- if (network == null) {
- tblMgr.addTable(metadata.getTable());
+ if (tblMgr.getTable(tbl.getSUID()) == null) {
+ tblMgr.addTable(tbl);
}
}
}
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportOntologyAndAnnotationTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportOntologyAndAnnotationTask.java
2012-04-03 19:34:03 UTC (rev 28729)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportOntologyAndAnnotationTask.java
2012-04-03 20:24:20 UTC (rev 28730)
@@ -20,7 +20,7 @@
private static final Logger logger =
LoggerFactory.getLogger(ImportOntologyAndAnnotationTask.class);
private final InputStreamTaskFactory factory;
- private final CyNetworkManager manager;
+ private final CyNetworkManager networkManager;
private final String ontologyDagName;
private final CyTableFactory tableFactory;
private final InputStream gaStream;
@@ -28,7 +28,7 @@
private final CyTableManager tableManager;
private final InputStream is;
- ImportOntologyAndAnnotationTask(final CyNetworkManager manager,
+ ImportOntologyAndAnnotationTask(final CyNetworkManager networkManager,
final InputStreamTaskFactory factory,
final InputStream is,
final String ontologyDagName,
final CyTableFactory tableFactory,
@@ -36,7 +36,7 @@
final CyTableManager tableManager)
{
this.factory = factory;
- this.manager = manager;
+ this.networkManager = networkManager;
this.ontologyDagName = ontologyDagName;
this.tableFactory = tableFactory;
@@ -53,12 +53,11 @@
Task loadOBOTask = factory.createTaskIterator(is,
ontologyDagName).next();
final GeneAssociationReader gaReader =
- new GeneAssociationReader(tableFactory,
ontologyDagName, gaStream,
- gaTableName, tableManager);
+ new GeneAssociationReader(tableFactory,
ontologyDagName, gaStream, gaTableName, tableManager);
- insertTasksAfterCurrentTask(new
MapGeneAssociationTask(gaReader, manager));
+ insertTasksAfterCurrentTask(new
MapGeneAssociationTask(gaReader, tableManager, networkManager));
insertTasksAfterCurrentTask(gaReader);
- insertTasksAfterCurrentTask(new
RegisterOntologyTask((CyNetworkReader) loadOBOTask, manager, ontologyDagName));
+ insertTasksAfterCurrentTask(new
RegisterOntologyTask((CyNetworkReader) loadOBOTask, networkManager,
ontologyDagName));
insertTasksAfterCurrentTask(loadOBOTask);
}
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
2012-04-03 19:34:03 UTC (rev 28729)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
2012-04-03 20:24:20 UTC (rev 28730)
@@ -8,7 +8,7 @@
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyIdentifiable;
+import org.cytoscape.model.CyTableManager;
import
org.cytoscape.tableimport.internal.reader.ontology.GeneAssociationReader;
import org.cytoscape.tableimport.internal.reader.ontology.OBOReader;
import org.cytoscape.work.AbstractTask;
@@ -22,9 +22,13 @@
final CyNetworkManager networkManager;
private final CyTableReader tableReader;
+ private final CyTableManager tableManager;
- MapGeneAssociationTask(final CyTableReader tableReader, final
CyNetworkManager networkManager) {
+ MapGeneAssociationTask(final CyTableReader tableReader,
+ final CyTableManager
tableManager,
+ final CyNetworkManager
networkManager) {
this.tableReader = tableReader;
+ this.tableManager = tableManager;
this.networkManager = networkManager;
}
@@ -38,6 +42,7 @@
if (tables == null || tables[0] == null)
throw new NullPointerException("Could not find table.");
+ tableManager.addTable(tables[0]);
mapping(taskMonitor, tables[0]);
}
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