Author: ruschein
Date: 2011-06-24 12:34:55 -0700 (Fri, 24 Jun 2011)
New Revision: 25923
Modified:
core3/search-impl/trunk/pom.xml
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchPlugin.java
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchQuery.java
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
Log:
Now invalid search expression errors are being displayed to the user and event
handling has been updated to the modern payload style. This fixes Redmine Bug
#134.
Modified: core3/search-impl/trunk/pom.xml
===================================================================
--- core3/search-impl/trunk/pom.xml 2011-06-24 18:58:29 UTC (rev 25922)
+++ core3/search-impl/trunk/pom.xml 2011-06-24 19:34:55 UTC (rev 25923)
@@ -94,22 +94,22 @@
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>model-api</artifactId>
- <version>3.0.0-alpha3</version>
+ <version>3.0.0-alpha5-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>viewmodel-api</artifactId>
- <version>3.0.0-alpha4</version>
+ <version>3.0.0-alpha5-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>core-task-api</artifactId>
- <version>3.0.0-alpha3</version>
+ <version>3.0.0-alpha4-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>session-api</artifactId>
- <version>3.0.0-alpha3</version>
+ <version>3.0.0-alpha6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape.wrappers</groupId>
@@ -120,13 +120,13 @@
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>swing-application-api</artifactId>
- <version>3.0.0-alpha2</version>
+ <version>3.0.0-alpha3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>work-swing-api</artifactId>
- <version>3.0.0-alpha2</version>
+ <version>3.0.0-alpha3-SNAPSHOT</version>
</dependency>
<!-- dependencies specifically for unit testing -->
Modified:
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
===================================================================
---
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
2011-06-24 18:58:29 UTC (rev 25922)
+++
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
2011-06-24 19:34:55 UTC (rev 25923)
@@ -1,5 +1,5 @@
/*
- Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2006, 2007, 2010, 2011, The Cytoscape Consortium
(www.cytoscape.org)
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
@@ -96,7 +96,6 @@
* attribute fields
*/
private static Document createDocument(CyTableEntry graphObject, String
graphObjectType, int index) {
-
Document doc = new Document();
String identifier = Integer.toString(index);
@@ -146,9 +145,13 @@
doc.add(new Field(attrIndexingName, attrValue,
Field.Store.YES, Field.Index.ANALYZED));
} else if (valueType == List.class) {
List attrValueList =
graphObject.getCyRow().get(attrName, List.class);
- for (int j = 0; j < attrValueList.size(); j++) {
- String attrValue =
attrValueList.get(j).toString();
- doc.add(new Field(attrIndexingName,
attrValue, Field.Store.YES, Field.Index.ANALYZED));
+ if (attrValueList != null) {
+ for (int j = 0; j <
attrValueList.size(); j++) {
+ String attrValue =
attrValueList.get(j).toString();
+ doc.add(new
Field(attrIndexingName, attrValue,
+
Field.Store.YES,
+
Field.Index.ANALYZED));
+ }
}
}
}
@@ -159,5 +162,4 @@
public RAMDirectory getIndex() {
return idx;
}
-
}
Modified:
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchPlugin.java
===================================================================
---
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchPlugin.java
2011-06-24 18:58:29 UTC (rev 25922)
+++
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchPlugin.java
2011-06-24 19:34:55 UTC (rev 25923)
@@ -1,14 +1,6 @@
-
/*
- Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2006, 2007, 2011, The Cytoscape Consortium (www.cytoscape.org)
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 2.1 of the License, or
@@ -32,15 +24,18 @@
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
+*/
package org.cytoscape.search.internal;
+
+import java.awt.Component;
+
+import org.cytoscape.application.swing.AbstractToolBarComponent;
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedEvent;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedListener;
-import org.cytoscape.model.events.RowsAboutToChangeEvent;
-import org.cytoscape.model.events.RowsFinishedChangingEvent;
import org.cytoscape.session.CyApplicationManager;
import org.cytoscape.session.events.SessionLoadedEvent;
import org.cytoscape.session.events.SessionLoadedListener;
@@ -49,27 +44,28 @@
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.search.internal.ui.EnhancedSearchPanel;
import org.cytoscape.work.swing.GUITaskManager;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.application.swing.AbstractToolBarComponent;
-import org.cytoscape.event.CyEventHelper;
-import java.awt.Component;
-public class EnhancedSearchPlugin extends AbstractToolBarComponent implements
SetCurrentNetworkViewListener, NetworkAboutToBeDestroyedListener,
- SessionLoadedListener
+public class EnhancedSearchPlugin extends AbstractToolBarComponent
+ implements SetCurrentNetworkViewListener,
NetworkAboutToBeDestroyedListener,
+ SessionLoadedListener
{
- private EnhancedSearchManager searchMgr = null;
- private EnhancedSearchPanel searchPnl = null;
- public static CyEventHelper eventHelper;
+ private final EnhancedSearchManager searchMgr;
+ private final EnhancedSearchPanel searchPnl;
+ static CyEventHelper eventHelper;
- public EnhancedSearchPlugin(CySwingApplication desktopApp,
CyApplicationManager netmgr,
- CyTableManager tableMgr, GUITaskManager taskMgr, final
CyEventHelper eventHelper) {
+ public EnhancedSearchPlugin(final CySwingApplication desktopApp,
+ final CyApplicationManager netmgr,
+ final CyTableManager tableMgr,
+ final GUITaskManager taskMgr,
+ final CyEventHelper eventHelper)
+ {
searchMgr = new EnhancedSearchManager();
// Add a text-field and a search button on tool-bar
searchPnl = new EnhancedSearchPanel(netmgr, tableMgr,
searchMgr, taskMgr);
this.setToolBarGravity(150.0f);
- EnhancedSearchPlugin.eventHelper = eventHelper;
+ EnhancedSearchPlugin.eventHelper = eventHelper;
}
@Override
Modified:
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchQuery.java
===================================================================
---
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchQuery.java
2011-06-24 18:58:29 UTC (rev 25922)
+++
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchQuery.java
2011-06-24 19:34:55 UTC (rev 25923)
@@ -1,13 +1,6 @@
/*
- Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2006, 2007, 2011, The Cytoscape Consortium (www.cytoscape.org)
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 2.1 of the License, or
@@ -31,39 +24,40 @@
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
+*/
package org.cytoscape.search.internal;
+
import java.io.IOException;
import java.util.ArrayList;
+import javax.swing.JOptionPane;
+
import org.apache.lucene.analysis.standard.StandardAnalyzer;
-import org.apache.lucene.queryParser.ParseException;
+import org.apache.lucene.document.Document;
+import org.apache.lucene.index.IndexReader;
+import org.apache.lucene.search.Collector;
import org.apache.lucene.search.IndexSearcher;
-import org.apache.lucene.search.Query;
+import org.apache.lucene.search.Scorer;
import org.apache.lucene.search.Searcher;
+import org.apache.lucene.search.Query;
import org.apache.lucene.store.RAMDirectory;
-import org.apache.lucene.document.Document;
-import org.cytoscape.search.internal.util.EnhancedSearchUtils;
-import org.cytoscape.search.internal.util.CustomMultiFieldQueryParser;
-import org.cytoscape.search.internal.util.AttributeFields;
+import org.apache.lucene.queryParser.ParseException;
+import org.apache.lucene.util.Version;
+
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyTableManager;
-import org.apache.lucene.util.Version;
-import org.apache.lucene.search.Collector;
-import org.apache.lucene.index.IndexReader;
-import org.apache.lucene.search.Scorer;
+import org.cytoscape.search.internal.util.AttributeFields;
+import org.cytoscape.search.internal.util.CustomMultiFieldQueryParser;
+import org.cytoscape.search.internal.util.EnhancedSearchUtils;
public class EnhancedSearchQuery {
-
+ private final RAMDirectory idx;
+ private final CyNetwork network;
+ private final CyTableManager tableMgr;
private IdentifiersCollector hitCollector = null;
+ private Searcher searcher = null;
- private RAMDirectory idx;
- private CyNetwork network;
- private Searcher searcher;
- private CyTableManager tableMgr;
-
public EnhancedSearchQuery(CyNetwork network, RAMDirectory index,
CyTableManager tableMgr) {
this.network = network;
this.idx = index;
@@ -72,7 +66,6 @@
public void executeQuery(String queryString) {
try {
-
// Define attribute fields in which the search is to be
carried on
AttributeFields attFields = new
AttributeFields(network, tableMgr);
@@ -94,32 +87,32 @@
* attributeName), search is carried out on all attribute fields. This
* functionality is enabled with the use of MultiFieldQueryParser.
*/
- private void search(String queryString, AttributeFields attFields)
- throws IOException {
-
+ private void search(final String queryString, final AttributeFields
attFields)
+ throws IOException
+ {
// Build a Query object.
// CustomMultiFieldQueryParser is used to support range queries
on numerical attribute fields.
- CustomMultiFieldQueryParser queryParser = new
CustomMultiFieldQueryParser(attFields, new StandardAnalyzer(Version.LUCENE_30));
+ final CustomMultiFieldQueryParser queryParser =
+ new CustomMultiFieldQueryParser(attFields, new
StandardAnalyzer(Version.LUCENE_30));
try {
// Execute query
Query query = queryParser.parse(queryString);
-
hitCollector = new IdentifiersCollector(searcher);
searcher.search(query, hitCollector);
- } catch (ParseException pe) {
+ } catch (final ParseException pe) {
// Parse exceptions occur when colon appear in the
query in an
// unexpected location, e.g. when attribute or value are
// missing in the query. In such case, the hitCollector
// variable will be null.
- System.out.println("Invalid query '" + queryString +
"'");
- String message = pe.getMessage();
- System.out.println(message);
- } catch (Exception e) {
+ JOptionPane.showMessageDialog(null, pe.getMessage(),
+ "Invalid query!",
+
JOptionPane.ERROR_MESSAGE);
+ } catch (final Exception e) {
// Other types of exception may occur
- System.out.println("Error during execution of query '"
+ queryString + "'");
- String message = e.getMessage();
- System.out.println(message);
+ JOptionPane.showMessageDialog(null, e.getMessage(),
+ "Query execution error!",
+
JOptionPane.ERROR_MESSAGE);
}
}
Modified:
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
===================================================================
---
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
2011-06-24 18:58:29 UTC (rev 25922)
+++
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
2011-06-24 19:34:55 UTC (rev 25923)
@@ -1,13 +1,6 @@
/*
- Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2006, 2007, 2011, The Cytoscape Consortium (www.cytoscape.org)
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 2.1 of the License, or
@@ -31,41 +24,41 @@
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
+*/
package org.cytoscape.search.internal;
+
import java.util.ArrayList;
import java.util.List;
import java.util.Iterator;
+
import org.apache.lucene.store.RAMDirectory;
+
import org.cytoscape.model.CyNetwork;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyEdge;
import org.cytoscape.task.AbstractNetworkViewTask;
import org.cytoscape.work.TaskMonitor;
-//import org.cytoscape.work.Tunable;
import org.cytoscape.model.CyTableManager;
-import org.cytoscape.model.events.RowsAboutToChangeEvent;
-import org.cytoscape.model.events.RowsFinishedChangingEvent;
-public class IndexAndSearchTask extends AbstractNetworkViewTask {
+public class IndexAndSearchTask extends AbstractNetworkViewTask {
private boolean interrupted = false;
private EnhancedSearch enhancedSearch;
private CyNetwork network;
private CyTableManager tableMgr;
- //@Tunable(description="Search for:")
public String query;
/**
- * The constructor. Any necessary data that is <i>not</i> provided by
- * the user should be provided as arguments to the constructor.
+ * The constructor. Any necessary data that is <i>not</i> provided by
+ * the user should be provided as arguments to the constructor.
*/
- public IndexAndSearchTask(final CyNetworkView networkView,
EnhancedSearch enhancedSearch,
- CyTableManager tableMgr, String query) {
+ public IndexAndSearchTask(final CyNetworkView networkView,
+ final EnhancedSearch enhancedSearch,
+ final CyTableManager tableMgr, String query)
+ {
// Will set a CyNetwork field called "net".
super(networkView);
network = networkView.getModel();
@@ -76,7 +69,6 @@
@Override
public void run(final TaskMonitor taskMonitor) {
-
// Give the task a title.
taskMonitor.setTitle("Searching the network");
@@ -85,49 +77,33 @@
String status = enhancedSearch.getNetworkIndexStatus(network);
- if (status != null &&
status.equalsIgnoreCase(EnhancedSearch.INDEX_SET)) {
- idx = enhancedSearch.getNetworkIndex(network);
- } else {
+ if (status != null &&
status.equalsIgnoreCase(EnhancedSearch.INDEX_SET))
+ idx = enhancedSearch.getNetworkIndex(network);
+ else {
taskMonitor.setStatusMessage("Indexing network");
EnhancedSearchIndex indexHandler = new
EnhancedSearchIndex(network);
idx = indexHandler.getIndex();
enhancedSearch.setNetworkIndex(network, idx);
}
- if (interrupted) {
+ if (interrupted)
return;
- }
// Execute query
taskMonitor.setStatusMessage("Executing query");
EnhancedSearchQuery queryHandler = new
EnhancedSearchQuery(network, idx, tableMgr);
queryHandler.executeQuery(query);
- if (interrupted) {
+ if (interrupted)
return;
- }
-
- if (network != null && network.getNodeList().size() > 0){
- try {
-
-
EnhancedSearchPlugin.eventHelper.fireSynchronousEvent(new
RowsAboutToChangeEvent(this, network.getDefaultNodeTable()));
-
EnhancedSearchPlugin.eventHelper.fireSynchronousEvent(new
RowsAboutToChangeEvent(this, network.getDefaultEdgeTable()));
-
- showResults(queryHandler, taskMonitor);
- }
- finally {
-
EnhancedSearchPlugin.eventHelper.fireAsynchronousEvent(new
RowsFinishedChangingEvent(this, network.getDefaultNodeTable()));
-
EnhancedSearchPlugin.eventHelper.fireAsynchronousEvent(new
RowsFinishedChangingEvent(this, network.getDefaultEdgeTable()));
- }
- }
}
-
- private void showResults(EnhancedSearchQuery queryHandler, final
TaskMonitor taskMonitor){
- // Display results
- if (network == null || network.getNodeList().size() == 0){
+ // Display results
+ private void showResults(final EnhancedSearchQuery queryHandler,
+ final TaskMonitor taskMonitor)
+ {
+ if (network == null || network.getNodeList().size() == 0)
return;
- }
List<CyNode> nodeList = network.getNodeList();
for (CyNode n : nodeList) {
@@ -140,9 +116,8 @@
int nodeHitCount = queryHandler.getNodeHitCount();
int edgeHitCount = queryHandler.getEdgeHitCount();
- if (nodeHitCount == 0 && edgeHitCount == 0) {
+ if (nodeHitCount == 0 && edgeHitCount == 0)
return;
- }
taskMonitor.setStatusMessage("Selecting " + nodeHitCount + "
and " + edgeHitCount + " edges");
@@ -154,11 +129,10 @@
while (nodeIt.hasNext() && !interrupted) {
int currESPIndex =
Integer.parseInt(nodeIt.next().toString());
CyNode currNode = network.getNode(currESPIndex);
- if (currNode != null) {
+ if (currNode != null)
currNode.getCyRow().set("selected", true);
- } else {
+ else
System.out.println("Unknown node identifier " +
(currESPIndex));
- }
taskMonitor.setProgress(numCompleted++ / nodeHitCount);
}
@@ -168,22 +142,20 @@
while (edgeIt.hasNext() && !interrupted) {
int currESPIndex =
Integer.parseInt(edgeIt.next().toString());
CyEdge currEdge = network.getEdge(currESPIndex);
- if (currEdge != null) {
+ if (currEdge != null)
currEdge.getCyRow().set("selected", true);
- } else {
+ else
System.out.println("Unknown edge identifier " +
(currESPIndex));
- }
- taskMonitor.setProgress(numCompleted++ / edgeHitCount);
+ taskMonitor.setProgress(++numCompleted / edgeHitCount);
}
// Refresh view to show selected nodes and edges
view.updateView();
}
-
@Override
public void cancel() {
this.interrupted = true;
}
-}
\ No newline at end of file
+}
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