Author: kono
Date: 2010-07-27 19:12:38 -0700 (Tue, 27 Jul 2010)
New Revision: 21042
Added:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ServiceState.java
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ui/SearchResultDialog.java
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/build.xml
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/plugin.props
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSI25VisualStyleBuilder.java
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSICQUICServiceRegistory.java
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSICQUICUniversalClient.java
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSICQUICUniversalClientPlugin.java
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/RegistryManager.java
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/mapper/Mitab25Mapper.java
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/mapper/PSIEntryMapper.java
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ui/ResultDialog.java
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/test/org/cytoscape/webservice/psicquic/test/RegistoryManagerTest.java
Log:
Version 0.25. New information dialog added and some bug fixes.
Modified: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/build.xml
===================================================================
--- csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/build.xml 2010-07-27
23:27:42 UTC (rev 21041)
+++ csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/build.xml 2010-07-28
02:12:38 UTC (rev 21042)
@@ -40,7 +40,9 @@
<!-- ==================== Compile Target
==============================-->
<target name="compile" depends="prepare" description="Compiles all Java
source files">
<mkdir dir="${build.dir}/classes" />
- <javac srcdir="${src.dir}" source="1.5" target="1.5"
destdir="${build.dir}/classes" debug="${compile.debug}"
deprecation="${compile.deprecation}" optimize="${compile.optimize}">
+ <javac srcdir="${src.dir}" source="1.5" target="1.5"
+ destdir="${build.dir}/classes" debug="${compile.debug}"
+ deprecation="${compile.deprecation}"
optimize="${compile.optimize}">
<classpath refid="compile.classpath" />
</javac>
</target>
Modified: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/plugin.props
===================================================================
--- csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/plugin.props
2010-07-27 23:27:42 UTC (rev 21041)
+++ csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/plugin.props
2010-07-28 02:12:38 UTC (rev 21042)
@@ -8,13 +8,13 @@
# Description used to give users information about the plugin such as what it
does.
# Html tags are encouraged for formatting purposes.
-pluginDescription=PSICQUIC Web Service Universal Client. You can perform
meta-search for <a href="http://code.google.com/p/psicquic/";>PSICQUIC data
service providers</a>. This plugin works with Cytoscape 2.7.0 (not released
yet) or later.
+pluginDescription=PSICQUIC Web Service Universal Client. You can perform
meta-search in PSICQUIC-compliant databases. This plugin works with Cytoscape
2.7.0 or later.
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=0.08
+pluginVersion=0.25
# Compatible Cytoscape version
-cytoscapeVersion=2.7
+cytoscapeVersion=2.7, 2.8
# Category, use one of the categories listed on the website or create your own
pluginCategory=Network and Attribute I/O
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSI25VisualStyleBuilder.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSI25VisualStyleBuilder.java
2010-07-27 23:27:42 UTC (rev 21041)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSI25VisualStyleBuilder.java
2010-07-28 02:12:38 UTC (rev 21042)
@@ -1,7 +1,9 @@
package org.cytoscape.webservice.psicquic;
import static cytoscape.visual.VisualPropertyType.NODE_LABEL;
+import giny.view.Justification;
import giny.view.Label;
+import giny.view.Position;
import java.awt.Color;
import java.awt.Font;
@@ -22,6 +24,7 @@
import cytoscape.visual.mappings.DiscreteMapping;
import cytoscape.visual.mappings.ObjectMapping;
import cytoscape.visual.mappings.PassThroughMapping;
+import ding.view.ObjectPositionImpl;
public class PSI25VisualStyleBuilder {
@@ -29,7 +32,7 @@
private static final String DEF_VS_NAME = "PSI-MI 25 Style";
// Prefix for all PSI-MI 25 attributes
- private static final String ATTR_PREFIX = "PSI-MI-25.";
+ public static final String ATTR_PREFIX = "PSI-MI-25.";
// Top level interaction types
private static final String[] ITR_TYPE_ROOT_TERMS = { "MI:0208",
"MI:0403",
@@ -61,9 +64,12 @@
// Default values
final int edgeOp = 160;
final Color nodeColor = new Color(0, 128, 128);
- final Color nodeLineColor = new Color(20, 20, 20);
+ final Color nodeLineColor = new Color(40, 40, 40);
final Color nodeLabelColor = new Color(30, 30, 30);
+ final Color nodeCompoundColor = new Color(100, 100, 100);
+ final Color nodeNestedColor = Color.white;
+
// final Color edgeColor = new Color(112,128,144);
final Color edgeColor = Color.black;
final Font nodeLabelFont = new Font("SansSerif.BOLD", 16,
Font.BOLD);
@@ -86,7 +92,7 @@
nodeColor);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_SHAPE,
NodeShape.RECT);
- nac.getDefaultAppearance().set(VisualPropertyType.NODE_OPACITY,
180);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_OPACITY,
150);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_BORDER_OPACITY,
220);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_LINE_WIDTH, 3);
@@ -98,13 +104,57 @@
nodeLabelColor);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_FONT_FACE,
nodeLabelFont);
+
nac.getDefaultAppearance().set(
VisualPropertyType.NODE_LABEL_POSITION,
new LabelPosition(Label.SOUTH, Label.NORTHWEST,
Label.JUSTIFY_CENTER, -7, 1.0));
+
+ // TODO: this is for 2.8.0
+// nac.getDefaultAppearance().set(
+// VisualPropertyType.NODE_LABEL_POSITION,
+// new ObjectPositionImpl(Position.SOUTH,
Position.NORTH_WEST,
+// Justification.JUSTIFY_CENTER,
-7, 1.0));
-
nac.getDefaultAppearance().set(VisualPropertyType.NODE_FONT_SIZE, 14);
+
nac.getDefaultAppearance().set(VisualPropertyType.NODE_FONT_SIZE, 10);
nac.setNodeSizeLocked(false);
+
+ DiscreteMapping nodeColorMapping = new
DiscreteMapping(nodeColor,
+ ATTR_PREFIX + "interactor type",
ObjectMapping.NODE_MAPPING);
+ nodeColorMapping.putMapValue("compound", nodeCompoundColor);
+ nodeColorMapping.putMapValue("nested", nodeNestedColor);
+ final Calculator nodeColorCalc = new
BasicCalculator(DEF_VS_NAME + "-"
+ + "NodeColorMapping", nodeColorMapping,
+ VisualPropertyType.NODE_FILL_COLOR);
+ nac.setCalculator(nodeColorCalc);
+
+ DiscreteMapping nodeShapeMapping = new
DiscreteMapping(NodeShape.RECT,
+ ATTR_PREFIX + "interactor type",
ObjectMapping.NODE_MAPPING);
+ nodeShapeMapping.putMapValue("compound", NodeShape.ELLIPSE);
+ nodeShapeMapping.putMapValue("nested", NodeShape.ROUND_RECT);
+ final Calculator nodeShapeCalc = new
BasicCalculator(DEF_VS_NAME + "-"
+ + "NodeShapeMapping", nodeShapeMapping,
+ VisualPropertyType.NODE_SHAPE);
+ nac.setCalculator(nodeShapeCalc);
+
+ DiscreteMapping nodeWidthMapping = new DiscreteMapping(30,
+ ATTR_PREFIX + "interactor type",
ObjectMapping.NODE_MAPPING);
+ nodeWidthMapping.putMapValue("compound", 15);
+ nodeWidthMapping.putMapValue("nested", 100);
+ final Calculator nodeWidthCalc = new
BasicCalculator(DEF_VS_NAME + "-"
+ + "NodeWidthMapping", nodeWidthMapping,
+ VisualPropertyType.NODE_WIDTH);
+ nac.setCalculator(nodeWidthCalc);
+ DiscreteMapping nodeHeightMapping = new DiscreteMapping(30,
+ ATTR_PREFIX + "interactor type",
ObjectMapping.NODE_MAPPING);
+ nodeHeightMapping.putMapValue("compound", 15);
+ nodeHeightMapping.putMapValue("nested", 100);
+ final Calculator nodeHeightCalc = new
BasicCalculator(DEF_VS_NAME + "-"
+ + "NodeHeightMapping", nodeHeightMapping,
+ VisualPropertyType.NODE_HEIGHT);
+ nac.setCalculator(nodeHeightCalc);
+
+
// eac.setCalculator(calce);
eac.getDefaultAppearance()
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSICQUICServiceRegistory.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSICQUICServiceRegistory.java
2010-07-27 23:27:42 UTC (rev 21041)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSICQUICServiceRegistory.java
2010-07-28 02:12:38 UTC (rev 21042)
@@ -33,8 +33,6 @@
public class PSICQUICServiceRegistory {
- private static RegistryManager manager;
-
private enum OperationType {
GET_COUNT, IMPORT;
}
@@ -43,7 +41,7 @@
private static Map<URI, String> serviceNames;
private static List<PsicquicService> ports;
- private Set<URI> emptyResults = new CopyOnWriteArraySet<URI>();
+ Set<URI> skip = new CopyOnWriteArraySet<URI>();
/*
* Initialize services. In 3.0, this will be done by Spring DM.
@@ -56,19 +54,17 @@
try {
// Human-readable database name should be taken from
PSI-MI 2.5
// ontology.
-
- manager = new RegistryManager();
-
- for (String serviceName :
manager.getRegistry().keySet()) {
+
+ for (String serviceName :
RegistryManager.getManager().getActiveServices().keySet()) {
final ClientProxyFactoryBean factory = new
JaxWsProxyFactoryBean();
factory.setServiceClass(PsicquicService.class);
-
factory.setAddress(manager.getRegistry().get(serviceName));
+
factory.setAddress(RegistryManager.getManager().getActiveServices().get(serviceName));
serviceNames.put(
- new
URI(manager.getRegistry().get(serviceName)),
+ new
URI(RegistryManager.getManager().getActiveServices().get(serviceName)),
serviceName);
final PsicquicService port = (PsicquicService)
factory.create();
ports.add(port);
- services.put(new
URI(manager.getRegistry().get(serviceName)),
+ services.put(new
URI(RegistryManager.getManager().getActiveServices().get(serviceName)),
port);
}
} catch (Exception e) {
@@ -128,7 +124,7 @@
System.out.println("Submit search query to " + key);
}
- emptyResults.clear();
+ skip.clear();
try {
for (int i = 0; i < services.size(); i++) {
res = cs.take();
@@ -140,7 +136,7 @@
+ ": Interactions Found
= "
+
qr.getResultInfo().getTotalResults());
if
(qr.getResultInfo().getTotalResults() == 0) {
- emptyResults.add(name);
+ skip.add(name);
}
}
}
@@ -192,7 +188,7 @@
// Submit tasks
Object port;
for (URI key : services.keySet()) {
- if (emptyResults.contains(key))
+ if (skip.contains(key))
continue;
port = services.get(key);
@@ -204,16 +200,16 @@
cs.submit(new PSICQUICRemoteTask(interactors,
reqInfo,
operator, port, key,
OperationType.IMPORT));
}
- System.out.println("Submit search query to " + key);
+ System.out.println("Submit import request to " + key);
}
try {
- for (int i = 0; i < services.size() -
emptyResults.size(); i++) {
+ for (int i = 0; i < services.size() - skip.size(); i++)
{
res = cs.take();
URI name = (URI) res.get().get(0);
- if (emptyResults.contains(name))
+ if (skip.contains(name))
continue;
final List<QueryResponse> qrList = new
ArrayList<QueryResponse>();
@@ -251,13 +247,13 @@
}
protected boolean isEmpty(final URI serviceURI) {
- if (this.emptyResults.contains(serviceURI))
+ if (this.skip.contains(serviceURI))
return true;
else
return false;
}
- class PSICQUICRemoteTask implements Callable<List<Object>>,
+ static final class PSICQUICRemoteTask implements Callable<List<Object>>,
CyWebServiceEventListener {
List<DbRef> interactorList;
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSICQUICUniversalClient.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSICQUICUniversalClient.java
2010-07-27 23:27:42 UTC (rev 21041)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSICQUICUniversalClient.java
2010-07-28 02:12:38 UTC (rev 21042)
@@ -10,12 +10,15 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.regex.Pattern;
+import javax.swing.JDialog;
import javax.swing.JPanel;
import org.cytoscape.webservice.psicquic.mapper.Mitab25Mapper;
import org.cytoscape.webservice.psicquic.ui.ResultDialog;
+import org.cytoscape.webservice.psicquic.ui.SearchResultDialog;
import org.hupo.psi.mi.psicquic.DbRef;
import org.hupo.psi.mi.psicquic.QueryResponse;
import org.hupo.psi.mi.psicquic.RequestInfo;
@@ -70,16 +73,14 @@
// General setting
props.add(new Tunable("block_size", "Block Size",
Tunable.INTEGER,
- new Integer(100)));
+ Integer.valueOf(100)));
props.add(new Tunable("timeout", "Timeout (sec.)",
Tunable.INTEGER,
new Integer(6000)));
- props.add(new Tunable("active_only", "Active Services Only",
- Tunable.BOOLEAN, new Boolean(true)));
final String[] modeArray = { QueryMode.GET_BY_INTERACTOR.name(),
QueryMode.GET_BY_QUERY.toString() };
props.add(new Tunable("query_mode", "Query Mode", Tunable.LIST,
- new Integer(0), (Object) modeArray, (Object)
null, 0));
+ Integer.valueOf(0), (Object) modeArray,
(Object) null, 0));
}
@@ -102,6 +103,8 @@
private Map<URI, QueryResponse> sResult;
private List<DbRef> queryList;
private String query;
+
+ private final ServiceState states;
static {
try {
@@ -119,6 +122,9 @@
setDescription();
// Set properties for this client.
setProperty();
+
+ this.states = new ServiceState(((PSICQUICServiceRegistory)
clientStub));
+
}
public static WebServiceClient<PSICQUICServiceRegistory> getClient() {
@@ -135,9 +141,16 @@
if (e.getSource().equals(CLIENT_ID)) {
if
(e.getEventType().equals(WSEventType.IMPORT_NETWORK)) {
- importNetwork(e.getParameter(), null);
+ SearchResultDialog searchResultDialog = new
SearchResultDialog(Cytoscape.getDesktop(), states);
+ searchResultDialog.setVisible(true);
+ Set<String> selected =
searchResultDialog.getSelected();
+
+ importNetwork(selected, null);
} else if
(e.getEventType().equals(WSEventType.EXPAND_NETWORK)) {
- importNetwork(e.getParameter(),
Cytoscape.getCurrentNetwork());
+ SearchResultDialog searchResultDialog = new
SearchResultDialog(Cytoscape.getDesktop(), states);
+ searchResultDialog.setVisible(true);
+ Set<String> selected =
searchResultDialog.getSelected();
+ importNetwork(selected,
Cytoscape.getCurrentNetwork());
} else if
(e.getEventType().equals(WSEventType.SEARCH_DATABASE)) {
search(e.getParameter().toString(), e);
}
@@ -188,19 +201,32 @@
nextMove = WSEventType.IMPORT_NETWORK;
Integer total = 0;
- for (URI key : sResult.keySet())
+ for (URI key : sResult.keySet()) {
+ final Integer count =
sResult.get(key).getResultInfo().getTotalResults();
+
states.setRecentResultCount(states.getName(key.toString()), count);
total = total +
sResult.get(key).getResultInfo().getTotalResults();
-
+ }
+
Cytoscape.firePropertyChange(SEARCH_FINISHED.toString(),
this.clientID,
new DatabaseSearchResult<Map<URI,
QueryResponse>>(total,
sResult, nextMove));
}
- private void importNetwork(Object result, CyNetwork e)
+ private void importNetwork(Set<String> selected, CyNetwork e)
throws CyWebServiceException {
+
+ if(selected == null || selected.size() == 0)
+ return;
PSICQUICServiceRegistory importClient =
((PSICQUICServiceRegistory) clientStub);
+ for(URI uri:importClient.getServiceNames().keySet()) {
+ String name = importClient.getServiceNames().get(uri);
+ if(selected.contains(name) == false)
+ importClient.skip.add(uri);
+ }
+
+
Map<URI, List<QueryResponse>> importResult = null;
final RequestInfo info = new RequestInfo();
@@ -291,6 +317,9 @@
targetView.redrawGraph(true, false);
CyNode nestedNode = Cytoscape.getCyNode(net.getTitle(),
true);
nestedNode.setNestedNetwork(net);
+
+
Cytoscape.getNodeAttributes().setAttribute(nestedNode.getIdentifier(),
PSI25VisualStyleBuilder.ATTR_PREFIX + "interactor type", "nested");
+
parentNetwork.addNode(nestedNode);
parentNetwork.addEdge(Cytoscape.getCyEdge(nestedNode,
centerNode, "interaction", "query_result", true));
}
@@ -360,5 +389,9 @@
}
return interactorList;
}
+
+ public void getLatestSearchResult() {
+
+ }
}
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSICQUICUniversalClientPlugin.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSICQUICUniversalClientPlugin.java
2010-07-27 23:27:42 UTC (rev 21041)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSICQUICUniversalClientPlugin.java
2010-07-28 02:12:38 UTC (rev 21042)
@@ -1,8 +1,13 @@
package org.cytoscape.webservice.psicquic;
+import java.awt.Component;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import cytoscape.Cytoscape;
import cytoscape.data.webservice.WebServiceClientManager;
import cytoscape.logger.CyLogger;
import cytoscape.plugin.CytoscapePlugin;
@@ -15,33 +20,63 @@
*
* @author kono
* @since Cytoscape 2.7
- *
+ *
*/
public class PSICQUICUniversalClientPlugin extends CytoscapePlugin {
+
+ private static final String TARGET_MENU = "Network from Web
Services...";
+ private static final CyLogger logger = CyLogger.getLogger();
+
public PSICQUICUniversalClientPlugin() {
+
+ // Disable menu until initialization process ends.
+
+ final JMenu importMenu =
Cytoscape.getDesktop().getCyMenus().getMenuBar().getMenu("File.Import");
+ final Component[] menues = importMenu.getMenuComponents();
+ JMenuItem webServiceMenu = null;
+
+ for(Component menu: menues) {
+ if(menu instanceof JMenuItem) {
+ JMenuItem menuItem = (JMenuItem) menu;
+ if(menuItem.getText().contains(TARGET_MENU)) {
+ webServiceMenu = menuItem;
+ break;
+ }
+ }
+ }
+
+ if(webServiceMenu != null) {
+ webServiceMenu.setEnabled(false);
+ webServiceMenu.setToolTipText("Initializing web service
clients. Please wait...");
+ }
+ final ExecutorService ex = Executors.newSingleThreadExecutor();
+
try {
-
- final ExecutorService ex =
Executors.newSingleThreadExecutor();
- System.out.println("Initializatin process start in separate
thread for PSICQUIC");
- ex.execute(new InitTask());
-
+ logger.info("Initializatin process start in separate
thread for PSICQUIC.");
+ ex.execute(new InitTask(webServiceMenu));
} catch (Exception e) {
- CyLogger.getLogger().error(
- "Failed to register PSICQUIC Universal
client.", e);
+ logger.error("Failed to initialize PSICQUIC Universal
Client.", e);
+ webServiceMenu.setEnabled(true);
+ webServiceMenu.setToolTipText(null);
}
-
-
+ }
- }
class InitTask implements Runnable {
+
+ private final JMenuItem menuItem;
+
+ InitTask(JMenuItem menu) {
+ this.menuItem = menu;
+ }
public void run() {
WebServiceClientManager.registerClient(PSICQUICUniversalClient
.getClient());
+ menuItem.setEnabled(true);
+ menuItem.setToolTipText(null);
}
-
}
}
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/RegistryManager.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/RegistryManager.java
2010-07-27 23:27:42 UTC (rev 21041)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/RegistryManager.java
2010-07-28 02:12:38 UTC (rev 21042)
@@ -29,31 +29,65 @@
*
*/
public class RegistryManager {
-
+
+ private static RegistryManager manager;
+
+ static {
+ try {
+ manager = new RegistryManager();
+ } catch (IOException e) {
+ manager = null;
+ e.printStackTrace();
+ }
+ }
+
+ public static RegistryManager getManager() {
+ return manager;
+ }
+
// Tag definitions
private static final String SOAP_URL = "soapUrl";
+ private static final String IS_ACTIVE = "active";
private static final String SERVICE_URL =
"http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry";;
-
- //Defines action command
+
+ // Defines action command
public enum STATE {
ACTIVE, INACTIVE, STATUS;
}
- private final Map<String, String> regMap;
+ private final Map<String, String> activeServiceMap;
+ private final Map<String, String> inactiveServiceMap;
+
+ private final Map<String, Boolean> statusMap;
+ private final Map<String, String> urlMap;
- public RegistryManager() throws IOException {
- regMap = new HashMap<String, String>();
+ private RegistryManager() throws IOException {
+ activeServiceMap = new HashMap<String, String>();
+ inactiveServiceMap = new HashMap<String, String>();
+ statusMap = new HashMap<String, Boolean>();
+ urlMap = new HashMap<String, String>();
invoke();
}
- public Map<String, String> getRegistry() {
- return regMap;
+ public Map<String, String> getActiveServices() {
+ return activeServiceMap;
}
-
+ public Map<String, String> getInactiveServices() {
+ return inactiveServiceMap;
+ }
+
private void invoke() throws IOException {
- String command = "?action=" + STATE.ACTIVE.name()
+"&format=xml";
+ final String command = "?action=" + STATE.STATUS.name() +
"&format=xml";
+ callRegistry(command);
+
+ setMap();
+
+ System.out.println("PSICQUIC Registory Manager is ready.");
+ }
+
+ private void callRegistry(final String command) throws IOException {
URL url = new URL(SERVICE_URL + command);
HttpURLConnection connection = (HttpURLConnection)
url.openConnection();
connection.setRequestMethod("GET");
@@ -73,27 +107,27 @@
builder.append(next);
}
+ reader.close();
+ reader = null;
+
try {
parse(builder.toString());
} catch (ParserConfigurationException e) {
-
+
e.printStackTrace();
throw new IOException("Could not parse message from
registry.");
} catch (XPathException e) {
- // TODO Auto-generated catch block
e.printStackTrace();
throw new IOException("Could not parse message from
registry.");
} catch (SAXException e) {
- // TODO Auto-generated catch block
e.printStackTrace();
throw new IOException("Could not parse message from
registry.");
}
-
- System.out.println("PSICQUIC Registory Manager is ready.");
}
- private void parse(String result) throws ParserConfigurationException,
IOException, XPathException, SAXException {
+ private void parse(String result) throws ParserConfigurationException,
+ IOException, XPathException, SAXException {
DocumentBuilderFactory dbfactory =
DocumentBuilderFactory.newInstance();
DocumentBuilder docbuilder = dbfactory.newDocumentBuilder();
@@ -111,7 +145,8 @@
for (int i = 0; i < list.getLength(); i++) {
regName = list.item(i).getFirstChild().getFirstChild()
.getNodeValue();
- System.out.println("Service Provider " + i + ": " +
regName);
+ System.out.println("Service Provider " + i + ": " +
regName);
+
walk(list.item(i), regName);
}
@@ -119,16 +154,31 @@
private void walk(Node item, String serviceName) {
- String tag = null;
- for(Node n = item.getFirstChild(); n!=null; n =
n.getNextSibling()) {
- tag = item.getNodeName();
- if(tag.equals(SOAP_URL)) {
- System.out.println("SOAP = "
- +
item.getFirstChild().getNodeValue());
- regMap.put(serviceName,
item.getFirstChild().getNodeValue());
- return;
- }
- walk(n, serviceName);
- }
+ String tag = null;
+
+ for (Node n = item.getFirstChild(); n != null; n =
n.getNextSibling()) {
+ tag = item.getNodeName();
+ if (tag.equals(SOAP_URL)) {
+ System.out.println("SOAP = "
+ +
item.getFirstChild().getNodeValue());
+ urlMap.put(serviceName,
item.getFirstChild().getNodeValue());
+
+ } else if (tag.equals(IS_ACTIVE)) {
+ System.out.println("Active? = "
+ +
item.getFirstChild().getNodeValue());
+ statusMap.put(serviceName,
Boolean.parseBoolean(item.getFirstChild().getNodeValue()));
+ }
+ walk(n, serviceName);
+ }
}
+
+ private void setMap() {
+ for(String serviceName: statusMap.keySet()){
+ System.out.println("######## Complete for " +
serviceName + " = " + statusMap.get(serviceName));
+ if (statusMap.get(serviceName) == true)
+ activeServiceMap.put(serviceName,
urlMap.get(serviceName));
+ else
+ inactiveServiceMap.put(serviceName,
urlMap.get(serviceName));
+ }
+ }
}
Added:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ServiceState.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ServiceState.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ServiceState.java
2010-07-28 02:12:38 UTC (rev 21042)
@@ -0,0 +1,60 @@
+package org.cytoscape.webservice.psicquic;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+public class ServiceState {
+ private final SortedSet<String> services;
+ private final Map<String, Integer> lastCounts;
+
+ private final Map<String, String> uri2name;
+
+
+ public ServiceState(PSICQUICServiceRegistory reg) {
+ services = new
TreeSet<String>(RegistryManager.getManager().getActiveServices().keySet());
+
services.addAll(RegistryManager.getManager().getInactiveServices().keySet());
+
+ uri2name = new HashMap<String, String>();
+ for(String serviceName:
RegistryManager.getManager().getActiveServices().keySet()) {
+
uri2name.put(RegistryManager.getManager().getActiveServices().get(serviceName),
serviceName);
+ }
+
+ lastCounts = new HashMap<String, Integer>();
+
+ }
+
+ public boolean isActive(final String serviceName) {
+
if(RegistryManager.getManager().getInactiveServices().keySet().contains(serviceName))
+ return false;
+ else
+ return true;
+
+ }
+
+ public Collection<String> getServiceNames() {
+ return services;
+ }
+
+ public int getRecentResultCount(final String serviceName) {
+ Integer count = lastCounts.get(serviceName);
+
+ if(count != null)
+ return count;
+ else
+ return 0;
+ }
+
+ public void setRecentResultCount(final String serviceName, Integer
count) {
+ lastCounts.put(serviceName, count);
+ }
+
+ public String getName(String uriString) {
+ return this.uri2name.get(uriString);
+ }
+
+
+
+}
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/mapper/Mitab25Mapper.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/mapper/Mitab25Mapper.java
2010-07-27 23:27:42 UTC (rev 21041)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/mapper/Mitab25Mapper.java
2010-07-28 02:12:38 UTC (rev 21042)
@@ -12,6 +12,7 @@
import cytoscape.CyNode;
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
+import cytoscape.logger.CyLogger;
/**
* Map minimal set of information from MITAB25.
@@ -21,11 +22,14 @@
*/
public class Mitab25Mapper {
+ private static final CyLogger logger = CyLogger.getLogger();
+
// Separator for multiple entries.
private static final String SEPARATOR = "\\|";
-
private static final String ATTR_PREFIX = "PSI-MI-25.";
+ private static final int COLUMN_COUNT = 15;
+
final Set<CyNode> nodes;
final Set<CyEdge> edges;
@@ -47,11 +51,17 @@
+ "interaction type";
private static final String SOURCE_DB = ATTR_PREFIX + "source database";
private static final String INTERACTION_ID = ATTR_PREFIX + "Interaction
ID";
+ private static final String EDGE_SCORE = ATTR_PREFIX + "confidence
score";
// Stable IDs which maybe used for mapping later
private static final String UNIPROT = "uniprotkb";
private static final String ENTREZ_GENE = "entrezgene/locuslink";
private static final String ENTREZ_GENE_SYN = "entrez gene/locuslink";
+
+ private static final String CHEBI = "chebi";
+
+ private static final String INTERACTOR_TYPE = ATTR_PREFIX + "interactor
type";
+ private static final String COMPOUND = "compound";
private Matcher matcher;
@@ -65,81 +75,14 @@
networkAttr = Cytoscape.getNetworkAttributes();
}
- public CyNetwork map(String mitab, String networkName, CyNetwork
parentNetwork) {
+ public CyNetwork map(String mitab, String networkName,
+ CyNetwork parentNetwork) {
// Read the long string of MITAB
String[] lines = mitab.split("\n");
- String[] entry;
- String[] sourceID;
- String[] targetID;
+ parse(lines);
- String[] detectionMethods;
- CyNode source;
- CyNode target;
- CyEdge e;
-
- String[] sourceDB;
- String[] interactionID;
- String[] interactionType;
-
- for (String line : lines) {
- entry = line.split(TAB);
- if (entry == null || entry.length < 12)
- continue;
-
- sourceID = entry[0].split(SEPARATOR);
- targetID = entry[1].split(SEPARATOR);
-
- source = Cytoscape.getCyNode(sourceID[0], true);
- target = Cytoscape.getCyNode(targetID[0], true);
- nodes.add(source);
- nodes.add(target);
-
- // Aliases
- setAliases(nodeAttr, source.getIdentifier(), entry[0]
- .split(SEPARATOR));
- setAliases(nodeAttr, target.getIdentifier(), entry[1]
- .split(SEPARATOR));
- setAliases(nodeAttr, source.getIdentifier(), entry[2]
- .split(SEPARATOR));
- setAliases(nodeAttr, target.getIdentifier(), entry[3]
- .split(SEPARATOR));
- setAliases(nodeAttr, source.getIdentifier(), entry[4]
- .split(SEPARATOR));
- setAliases(nodeAttr, target.getIdentifier(), entry[5]
- .split(SEPARATOR));
-
- // Tax ID (pick first one only)
- setTaxID(nodeAttr, source.getIdentifier(), entry[9]
- .split(SEPARATOR)[0]);
- setTaxID(nodeAttr, target.getIdentifier(), entry[10]
- .split(SEPARATOR)[0]);
-
- sourceDB = entry[12].split(SEPARATOR);
- interactionID = entry[13].split(SEPARATOR);
-
- detectionMethods = entry[6].split(SEPARATOR);
- interactionType = entry[11].split(SEPARATOR);
- e = Cytoscape.getCyEdge(source, target, INTERACTION,
- interactionID[0], true);
- edges.add(e);
-
- setEdgeListAttribute(edgeAttr, e.getIdentifier(),
interactionType,
- INTERACTION_TYPE);
- setEdgeListAttribute(edgeAttr, e.getIdentifier(),
detectionMethods,
- DETECTION_METHOD);
- setEdgeListAttribute(edgeAttr, e.getIdentifier(),
sourceDB,
- SOURCE_DB);
-
- edgeAttr.setAttribute(e.getIdentifier(), INTERACTION_ID,
- interactionID[0]);
-
- setPublication(edgeAttr, e.getIdentifier(), entry[8]
- .split(SEPARATOR),
entry[7].split(SEPARATOR));
-
- }
-
// Create top attribues for important keys
List<String> currentAttr;
for (CyNode node : nodes) {
@@ -155,7 +98,7 @@
nodeAttr.setAttribute(node.getIdentifier(),
ATTR_PREFIX
+ ENTREZ_GENE + ".top",
currentAttr.get(0));
}
-
+
currentAttr =
nodeAttr.getListAttribute(node.getIdentifier(),
ATTR_PREFIX + ENTREZ_GENE_SYN);
if (currentAttr != null && currentAttr.size() != 0) {
@@ -176,6 +119,99 @@
}
}
+ private void parse(final String[] lines) {
+ String[] entry;
+ String[] sourceID;
+ String[] targetID;
+
+ String[] detectionMethods;
+ CyNode source;
+ CyNode target;
+ CyEdge e;
+
+ String[] sourceDB;
+ String[] interactionID;
+ String[] interactionType;
+
+ String[] edgeScore;
+
+ for (String line : lines) {
+ try {
+ entry = line.split(TAB);
+
+ // Validate entry list.
+ if (entry == null || entry.length <
COLUMN_COUNT)
+ continue;
+
+ sourceID = entry[0].split(SEPARATOR);
+ targetID = entry[1].split(SEPARATOR);
+
+ source = Cytoscape.getCyNode(sourceID[0], true);
+ target = Cytoscape.getCyNode(targetID[0], true);
+ nodes.add(source);
+ nodes.add(target);
+
+ // Set type if not protein
+ if(source.getIdentifier().contains(CHEBI))
+
nodeAttr.setAttribute(source.getIdentifier(), INTERACTOR_TYPE, COMPOUND);
+ if(target.getIdentifier().contains(CHEBI))
+
nodeAttr.setAttribute(target.getIdentifier(), INTERACTOR_TYPE, COMPOUND);
+
+ // Aliases
+ setAliases(nodeAttr, source.getIdentifier(),
+ entry[0].split(SEPARATOR));
+ setAliases(nodeAttr, target.getIdentifier(),
+ entry[1].split(SEPARATOR));
+ setAliases(nodeAttr, source.getIdentifier(),
+ entry[2].split(SEPARATOR));
+ setAliases(nodeAttr, target.getIdentifier(),
+ entry[3].split(SEPARATOR));
+ setAliases(nodeAttr, source.getIdentifier(),
+ entry[4].split(SEPARATOR));
+ setAliases(nodeAttr, target.getIdentifier(),
+ entry[5].split(SEPARATOR));
+
+ // Tax ID (pick first one only)
+ setTaxID(nodeAttr, source.getIdentifier(),
+ entry[9].split(SEPARATOR)[0]);
+ setTaxID(nodeAttr, target.getIdentifier(),
+ entry[10].split(SEPARATOR)[0]);
+
+ sourceDB = entry[12].split(SEPARATOR);
+ interactionID = entry[13].split(SEPARATOR);
+
+ edgeScore = entry[14].split(SEPARATOR);
+
+ detectionMethods = entry[6].split(SEPARATOR);
+ interactionType = entry[11].split(SEPARATOR);
+ e = Cytoscape.getCyEdge(source, target,
INTERACTION,
+ interactionID[0], true);
+ edges.add(e);
+
+ setEdgeListAttribute(edgeAttr,
e.getIdentifier(),
+ interactionType,
INTERACTION_TYPE);
+ setEdgeListAttribute(edgeAttr,
e.getIdentifier(),
+ detectionMethods,
DETECTION_METHOD);
+ setEdgeListAttribute(edgeAttr,
e.getIdentifier(), sourceDB,
+ SOURCE_DB);
+
+ // Map scores
+ setEdgeScoreListAttribute(edgeAttr,
e.getIdentifier(), edgeScore,
+ EDGE_SCORE);
+
+ edgeAttr.setAttribute(e.getIdentifier(),
INTERACTION_ID,
+ interactionID[0]);
+
+ setPublication(edgeAttr, e.getIdentifier(),
+ entry[8].split(SEPARATOR),
entry[7].split(SEPARATOR));
+ } catch (Exception ex) {
+ logger.warn("Invalid entry line found: " +
line, ex);
+ continue;
+ }
+
+ }
+ }
+
private void setNetworkAttr(final CyNetwork net) {
}
@@ -191,8 +227,8 @@
if (matcher.find()) {
taxonName = matcher.group();
attr.setAttribute(id, attrName,
buf[1].split("\\(")[0]);
- attr.setAttribute(id, attrName + ".name",
taxonName.substring(
- 1, taxonName.length() - 1));
+ attr.setAttribute(id, attrName + ".name",
+ taxonName.substring(1,
taxonName.length() - 1));
} else {
attr.setAttribute(id, attrName, buf[1]);
}
@@ -249,7 +285,36 @@
listAttrMapper(attr, key + ".name", id, name);
}
}
+
+ // Special case for edge scores
+ private void setEdgeScoreListAttribute(CyAttributes attr, String id,
+ String[] entry, String key) {
+ String scoreString;
+ String scoreType;
+
+ for (String val : entry) {
+ final String[] parts = val.split(":");
+ if(parts == null || parts.length != 2)
+ continue;
+
+ scoreString = parts[1];
+ scoreType = parts[0];
+
+ try {
+ final Double score =
Double.parseDouble(scoreString);
+ edgeAttr.setAttribute(id, key + "." +
scoreType, score);
+ } catch (Exception e) {
+ if(scoreString != null &&
scoreString.trim().equals("") == false)
+ edgeAttr.setAttribute(id, key + "." +
scoreType, scoreString);
+
+ continue;
+ }
+ }
+ }
+
+
+
private void listAttrMapper(CyAttributes attr, String attrName, String
id,
String value) {
List currentAttr;
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/mapper/PSIEntryMapper.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/mapper/PSIEntryMapper.java
2010-07-27 23:27:42 UTC (rev 21041)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/mapper/PSIEntryMapper.java
2010-07-28 02:12:38 UTC (rev 21042)
@@ -40,12 +40,12 @@
public void map(Entry entry) {
// Extract All
- AttributeList attrs = entry.getAttributeList();
- AvailabilityList availability = entry.getAvailabilityList();
- ExperimentDescriptionList expList = entry.getExperimentList();
+// AttributeList attrs = entry.getAttributeList();
+// AvailabilityList availability = entry.getAvailabilityList();
+// ExperimentDescriptionList expList = entry.getExperimentList();
InteractionList interactions = entry.getInteractionList();
InteractorList interactors = entry.getInteractorList();
- Source source = entry.getSource();
+// Source source = entry.getSource();
mapInteractors(interactors);
mapInteractions(interactions);
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ui/ResultDialog.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ui/ResultDialog.java
2010-07-27 23:27:42 UTC (rev 21041)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ui/ResultDialog.java
2010-07-28 02:12:38 UTC (rev 21042)
@@ -16,12 +16,16 @@
public class ResultDialog extends javax.swing.JDialog {
private static final long serialVersionUID = 6996385373168492882L;
+
private Map<URI, String> dbNames;
private DefaultTableModel model;
private boolean mergeNetworks;
- /** Creates new form PSICQUICResultDialog */
+ /**
+ * Creates new form PSICQUICResultDialog
+ *
+ */
public ResultDialog(Frame parent, boolean modal, Map<URI, String>
dbNames) {
super(parent, modal);
this.dbNames = dbNames;
@@ -42,7 +46,7 @@
});
model = (DefaultTableModel) resultTable.getModel();
- model.addColumn("Source", dbNames.keySet().toArray());
+ model.addColumn("Service URL", dbNames.keySet().toArray());
model.addColumn("Network Name (Please edit these if
necessary)");
for (int i = 0; i < model.getRowCount(); i++) {
model.setValueAt(dbNames.get(model.getValueAt(i, 0)),
i, 1);
Added:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ui/SearchResultDialog.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ui/SearchResultDialog.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ui/SearchResultDialog.java
2010-07-28 02:12:38 UTC (rev 21042)
@@ -0,0 +1,320 @@
+package org.cytoscape.webservice.psicquic.ui;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Frame;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.table.DefaultTableModel;
+import javax.swing.table.TableCellRenderer;
+
+import org.cytoscape.webservice.psicquic.ServiceState;
+
+public class SearchResultDialog extends javax.swing.JDialog {
+
+ private static final long serialVersionUID = 6996385373168492882L;
+
+ private DefaultTableModel model;
+
+ private final ServiceState state;
+
+ /**
+ * Creates new form PSICQUICResultDialog
+ *
+ */
+ public SearchResultDialog(Frame parent, final ServiceState states) {
+ super(parent, true);
+ this.state = states;
+
+ setTableModel();
+ initComponents();
+
+ setCoumnWidth();
+
+ pack();
+ this.setLocationRelativeTo(parent);
+ }
+
+ public Set<String> getSelected() {
+ final Set<String> selectedService = new HashSet<String>();
+
+ for(int i=0; i<model.getRowCount(); i++) {
+ Boolean selected = (Boolean) model.getValueAt(i, 0);
+
+ if(selected) {
+ selectedService.add(model.getValueAt(i,
1).toString());
+ }
+ }
+
+ return selectedService;
+ }
+
+ private void setCoumnWidth() {
+
+ resultTable.getTableHeader().setReorderingAllowed(false);
+ resultTable.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
+ // Checkbox
+ resultTable.getColumnModel().getColumn(0).setPreferredWidth(70);
+ // Name
+
resultTable.getColumnModel().getColumn(1).setPreferredWidth(200);
+ // Number of result
+
resultTable.getColumnModel().getColumn(2).setPreferredWidth(120);
+ // Status
+
resultTable.getColumnModel().getColumn(3).setPreferredWidth(100);
+
+ }
+
+ private void setTableModel() {
+ resultTable = new javax.swing.JTable(new DefaultTableModel() {
+
+ private static final long serialVersionUID =
-7798626850196524108L;
+
+ @Override
+ public boolean isCellEditable(int row, int column) {
+ final int count = (Integer)
model.getValueAt(row, 2);
+ final String active = model.getValueAt(row,
3).toString();
+
+ if (column == 0 && active.equals("Active") &&
count != 0)
+ return true;
+ else
+ return false;
+ }
+
+ public Class<?> getColumnClass(int c) {
+ return getValueAt(0, c).getClass();
+ }
+ });
+
+ model = (DefaultTableModel) resultTable.getModel();
+
+ model.addColumn("Import?");
+ model.addColumn("Service Name");
+ model.addColumn("Records Found");
+ model.addColumn("Status");
+
+ System.out.println("########Service count = "
+ + state.getServiceNames().size());
+ for (final String serviceName : state.getServiceNames()) {
+ Object[] vals = new Object[4];
+
+ vals[1] = serviceName;
+ vals[2] = state.getRecentResultCount(serviceName);
+
+ if (state.isActive(serviceName)) {
+ vals[3] = "Active";
+ if((Integer)vals[2] != 0)
+ vals[0] = true;
+ else
+ vals[0] = false;
+ } else {
+ vals[0] = false;
+ vals[3] = "Inactive";
+ }
+ model.addRow(vals);
+ }
+
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the
form.
+ * WARNING: Do NOT modify this code. The content of this method is
always
+ * regenerated by the Form Editor.
+ */
+ @SuppressWarnings("unchecked")
+ // <editor-fold defaultstate="collapsed" desc="Generated Code">
+ private void initComponents() {
+ setTitle("PSICQUIC Import Result");
+
+ titlePanel = new javax.swing.JPanel();
+ titleLabel = new javax.swing.JLabel();
+ resultScrollPane = new javax.swing.JScrollPane();
+
+ buttonPanel = new javax.swing.JPanel();
+ okButton = new javax.swing.JButton();
+ mergeButton = new javax.swing.JButton();
+ mergeButton = new javax.swing.JButton();
+
+
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+
+ titlePanel.setBackground(java.awt.Color.white);
+
+ titleLabel.setFont(new java.awt.Font("SansSerif", 1, 14)); //
NOI18N
+ titleLabel.setText("PSICQUIC DB Search Result");
+
+ org.jdesktop.layout.GroupLayout titlePanelLayout = new
org.jdesktop.layout.GroupLayout(
+ titlePanel);
+ titlePanel.setLayout(titlePanelLayout);
+ titlePanelLayout
+
.setHorizontalGroup(titlePanelLayout.createParallelGroup(
+
org.jdesktop.layout.GroupLayout.LEADING).add(
+
titlePanelLayout.createSequentialGroup()
+
.addContainerGap().add(titleLabel)
+
.addContainerGap(200, Short.MAX_VALUE)));
+
titlePanelLayout.setVerticalGroup(titlePanelLayout.createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING).add(
+ titlePanelLayout
+ .createSequentialGroup()
+ .addContainerGap()
+ .add(titleLabel)
+ .addContainerGap(
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
Short.MAX_VALUE)));
+
+ resultScrollPane.setBackground(java.awt.Color.white);
+
+ resultScrollPane.setViewportView(resultTable);
+
+ buttonPanel.setBackground(java.awt.Color.white);
+
+ okButton.setText("OK");
+ okButton.setPreferredSize(new java.awt.Dimension(70, 26));
+ okButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent
evt) {
+ okButtonActionPerformed(evt);
+ }
+ });
+
+ mergeButton.setText("Cancel");
+ mergeButton.setPreferredSize(new java.awt.Dimension(70, 26));
+ mergeButton.addActionListener(new
java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent
evt) {
+ dispose();
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout buttonPanelLayout = new
org.jdesktop.layout.GroupLayout(
+ buttonPanel);
+ buttonPanel.setLayout(buttonPanelLayout);
+ buttonPanelLayout
+ .setHorizontalGroup(buttonPanelLayout
+ .createParallelGroup(
+
org.jdesktop.layout.GroupLayout.LEADING)
+
.add(org.jdesktop.layout.GroupLayout.TRAILING,
+
buttonPanelLayout
+
.createSequentialGroup()
+
.addContainerGap(450, Short.MAX_VALUE)
+
.add(mergeButton,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+
.addPreferredGap(
+
org.jdesktop.layout.LayoutStyle.RELATED)
+
.add(okButton,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+
55,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+
.addContainerGap()));
+ buttonPanelLayout
+ .setVerticalGroup(buttonPanelLayout
+ .createParallelGroup(
+
org.jdesktop.layout.GroupLayout.LEADING)
+
.add(org.jdesktop.layout.GroupLayout.TRAILING,
+
buttonPanelLayout
+
.createSequentialGroup()
+
.addContainerGap(
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
Short.MAX_VALUE)
+
.add(buttonPanelLayout
+
.createParallelGroup(
+
org.jdesktop.layout.GroupLayout.BASELINE)
+
.add(okButton,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+
.add(mergeButton,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+
.addContainerGap()));
+
+ org.jdesktop.layout.GroupLayout layout = new
org.jdesktop.layout.GroupLayout(
+ getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(layout
+
.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(titlePanel,
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(resultScrollPane,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 480,
+ Short.MAX_VALUE)
+ .add(buttonPanel,
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE));
+ layout.setVerticalGroup(layout
+
.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout
+ .createSequentialGroup()
+ .add(titlePanel,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(
+
org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(resultScrollPane,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 250,
Short.MAX_VALUE)
+ .addPreferredGap(
+
org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(buttonPanel,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+
+ pack();
+ }// </editor-fold>
+
+ private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ this.dispose();
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JPanel buttonPanel;
+ private javax.swing.JButton mergeButton;
+ private javax.swing.JButton okButton;
+ private javax.swing.JScrollPane resultScrollPane;
+ private javax.swing.JTable resultTable;
+ private javax.swing.JLabel titleLabel;
+ private javax.swing.JPanel titlePanel;
+
+ // End of variables declaration
+
+ static class SearchResultTableRenderer implements TableCellRenderer {
+
+ public SearchResultTableRenderer() {
+ }
+
+ public Component getTableCellRendererComponent(JTable table,
+ Object value, boolean isSelected, boolean
hasFocus, int row,
+ int column) {
+
+ if (value == null)
+ return null;
+
+ Boolean target = (Boolean)
table.getModel().getValueAt(row, 0);
+
+ if (column == 0) {
+ JCheckBox checkBox = new JCheckBox();
+ checkBox.setSelected((Boolean) value);
+ if (target == false)
+ return checkBox;
+ } else {
+ JLabel label = new JLabel(value.toString());
+
+ if (target == false) {
+ label.setForeground(Color.red);
+ }
+ return label;
+ }
+
+ return null;
+
+ }
+ }
+
+}
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/test/org/cytoscape/webservice/psicquic/test/RegistoryManagerTest.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/test/org/cytoscape/webservice/psicquic/test/RegistoryManagerTest.java
2010-07-27 23:27:42 UTC (rev 21041)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/test/org/cytoscape/webservice/psicquic/test/RegistoryManagerTest.java
2010-07-28 02:12:38 UTC (rev 21042)
@@ -22,9 +22,8 @@
@Test
public void accessRegistory() throws Exception {
- RegistryManager rm = new RegistryManager();
- assertNotNull(rm.getRegistry());
+ assertNotNull(RegistryManager.getManager().getActiveServices());
}
}
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