Author: kono
Date: 2011-12-06 15:27:41 -0800 (Tue, 06 Dec 2011)
New Revision: 27720
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/CyActivator.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICRestClient.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICWebServiceClient.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
Log:
Cancellation code modified.
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/CyActivator.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/CyActivator.java
2011-12-06 22:55:50 UTC (rev 27719)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/CyActivator.java
2011-12-06 23:27:41 UTC (rev 27720)
@@ -2,17 +2,10 @@
import java.util.Properties;
-import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.CyTableFactory;
-import org.cytoscape.model.CyTableManager;
-import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.service.util.AbstractCyActivator;
-import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.task.NetworkTaskFactory;
-import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.swing.DialogTaskManager;
import org.osgi.framework.BundleContext;
@@ -23,28 +16,17 @@
public void start(BundleContext bc) {
- CyNetworkNaming namingService = getService(bc,
CyNetworkNaming.class);
DialogTaskManager tm = getService(bc, DialogTaskManager.class);
- CyApplicationManager cyApplicationManagerRef = getService(bc,
CyApplicationManager.class);
CyNetworkFactory cyNetworkFactoryServiceRef = getService(bc,
CyNetworkFactory.class);
- CyNetworkViewFactory cyNetworkViewFactoryServiceRef =
getService(bc, CyNetworkViewFactory.class);
CyNetworkManager cyNetworkManagerServiceRef = getService(bc,
CyNetworkManager.class);
- CyNetworkViewManager cyNetworkViewManagerServiceRef =
getService(bc, CyNetworkViewManager.class);
NetworkTaskFactory createViewTaskFactoryServiceRef =
getService(bc, NetworkTaskFactory.class,
"(id=createNetworkViewTaskFactory)");
- DialogTaskManager taskManagerServiceRef = getService(bc,
DialogTaskManager.class);
- CyTableManager cyTableManagerServiceRef = getService(bc,
CyTableManager.class);
- CyTableFactory cyDataTableFactoryServiceRef = getService(bc,
CyTableFactory.class);
- CyApplicationManager cyApplicationManagerServiceRef =
getService(bc, CyApplicationManager.class);
- CyRootNetworkManager cyRootNetworkFactoryServiceRef =
getService(bc, CyRootNetworkManager.class);
-
PSICQUICWebServiceClient psicquicClient = new
PSICQUICWebServiceClient(
"http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry";, "PSICQUIC
Universal Client",
- "REST version of PSICQUIC web service client.",
cyNetworkFactoryServiceRef,
- cyNetworkViewFactoryServiceRef,
cyNetworkViewManagerServiceRef, cyNetworkManagerServiceRef, tm,
- createViewTaskFactoryServiceRef);
+ "REST version of PSICQUIC web service client.",
cyNetworkFactoryServiceRef, cyNetworkManagerServiceRef,
+ tm, createViewTaskFactoryServiceRef);
registerAllServices(bc, psicquicClient, new Properties());
}
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICRestClient.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICRestClient.java
2011-12-06 22:55:50 UTC (rev 27719)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICRestClient.java
2011-12-06 23:27:41 UTC (rev 27720)
@@ -1,11 +1,8 @@
package org.cytoscape.webservice.psicquic;
import java.io.InputStream;
-import java.security.Timestamp;
-import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collection;
-import java.util.Date;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
@@ -21,11 +18,8 @@
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
-import javax.swing.SwingUtilities;
-
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.webservice.psicquic.mapper.CyNetworkBuilder;
@@ -63,18 +57,13 @@
private static final long IMPORT_TIMEOUT = 1000;
private final CyNetworkFactory factory;
- private final CyNetworkViewFactory viewFactory;
- private final CyNetworkViewManager viewManager;
- public PSICQUICRestClient(final CyNetworkFactory factory, final
CyNetworkViewFactory viewFactory,
- final CyNetworkViewManager viewManager) {
+ public PSICQUICRestClient(final CyNetworkFactory factory) {
this.factory = factory;
- this.viewFactory = viewFactory;
- this.viewManager = viewManager;
}
public Map<String, CyNetwork> importNetwork(final String query, final
Collection<String> targetServices,
- final SearchMode mode, final TaskMonitor tm) throws
InterruptedException {
+ final SearchMode mode, final TaskMonitor tm) {
final Map<String, CyNetwork> resultMap = new
ConcurrentHashMap<String, CyNetwork>();
final ExecutorService exe = Executors.newFixedThreadPool(20);
final CompletionService<Map<CyNetwork, String>>
completionService = new ExecutorCompletionService<Map<CyNetwork, String>>(exe);
@@ -84,10 +73,8 @@
// Submit the query for each active service
double completed = 0.0d;
final double increment = 1.0d / (double) targetServices.size();
- final List<ImportNetworkTask> tasks = new
ArrayList<ImportNetworkTask>();
for (final String serviceURL : targetServices)
completionService.submit(new
ImportNetworkTask(serviceURL, query, mode));
-
for (int i = 0; i < targetServices.size(); i++) {
try {
@@ -98,9 +85,11 @@
resultMap.put(source, network);
completed = completed + increment;
tm.setProgress(completed);
+ tm.setStatusMessage("Got " + i + " out of " +
targetServices.size() + " retults from remote database.");
} catch (InterruptedException ie) {
- logger.warn("Interrupted: network import", ie);
- continue;
+ logger.warn("!!! Interrupted: network import",
ie);
+ exe.shutdown();
+ return resultMap;
} catch (ExecutionException e) {
logger.warn("Error occured in network import",
e);
continue;
@@ -110,12 +99,12 @@
try {
exe.shutdown();
exe.awaitTermination(IMPORT_TIMEOUT, TimeUnit.SECONDS);
-
long endTime = System.currentTimeMillis();
double sec = (endTime - startTime) / (1000.0);
logger.info("PSICUQIC Import Finished in " + sec + "
sec.");
} catch (Exception ex) {
logger.warn("Import operation timeout", ex);
+ return resultMap;
}
return resultMap;
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICWebServiceClient.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICWebServiceClient.java
2011-12-06 22:55:50 UTC (rev 27719)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICWebServiceClient.java
2011-12-06 23:27:41 UTC (rev 27720)
@@ -53,8 +53,7 @@
private SearchRecoredsTask searchTask;
public PSICQUICWebServiceClient(final String uri, final String
displayName, final String description,
- final CyNetworkFactory networkFactory, final
CyNetworkViewFactory viewFactory,
- final CyNetworkViewManager viewManager, final
CyNetworkManager networkManager, final TaskManager tManager,
+ final CyNetworkFactory networkFactory, final
CyNetworkManager networkManager, final TaskManager tManager,
final NetworkTaskFactory createViewTaskFactory) {
super(uri, displayName, description);
@@ -62,7 +61,7 @@
this.tManager = tManager;
this.createViewTaskFactory = createViewTaskFactory;
- client = new PSICQUICRestClient(networkFactory, viewFactory,
viewManager);
+ client = new PSICQUICRestClient(networkFactory);
// Initialize registry manager in different thread.
initRegmanager();
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
2011-12-06 22:55:50 UTC (rev 27719)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
2011-12-06 23:27:41 UTC (rev 27720)
@@ -102,11 +102,9 @@
addNetworkData(network);
manager.addNetwork(network);
networks.add(network);
- }
-
+ }
- int retValue = JOptionPane.showConfirmDialog(null, "Do you want
to create view?");
-
+ int retValue = JOptionPane.showConfirmDialog(null, "Do you want
to create views?");
if(retValue == JOptionPane.YES_OPTION) {
// Create View
for(final CyNetwork network: networks) {
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