Author: pwang
Date: 2011-08-23 17:26:19 -0700 (Tue, 23 Aug 2011)
New Revision: 26628
Removed:
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/util/CytoscapeVersion.java
Modified:
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/DownloadableInfo.java
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/PluginManager.java
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/action/PluginManagerAction.java
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/ui/PluginManageDialog.java
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/ui/PluginUrlDialog.java
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/ui/TreeCellRenderer.java
core3/impl/trunk/plugin-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/impl/trunk/plugin-impl/src/main/resources/META-INF/spring/bundle-context.xml
Log:
Fixed bug #348
Modified:
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/DownloadableInfo.java
===================================================================
---
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/DownloadableInfo.java
2011-08-23 19:53:34 UTC (rev 26627)
+++
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/DownloadableInfo.java
2011-08-24 00:26:19 UTC (rev 26628)
@@ -38,8 +38,8 @@
import java.net.URL;
import java.io.IOException;
+import org.cytoscape.plugin.internal.action.PluginManagerAction;
import org.cytoscape.plugin.internal.util.URLUtil;
-import org.cytoscape.plugin.internal.util.CytoscapeVersion;
import static org.cytoscape.plugin.internal.PluginVersionUtils.versionOk;
import static org.cytoscape.plugin.internal.PluginVersionUtils.getNewerVersion;
@@ -400,7 +400,7 @@
if (pluginVersion == null )
return false;
- String[] cyVersion = new
CytoscapeVersion().getFullVersion().split(versionSplit);
+ String[] cyVersion =
PluginManagerAction.cyVersion.getVersion().split(versionSplit);
String[] plVersion = pluginVersion.split(versionSplit);
if ( cyVersion.length < plVersion.length )
@@ -438,9 +438,8 @@
}
boolean compatible = false;
- CytoscapeVersion cv = new CytoscapeVersion();
for (String pluginVersion: compatibleCyVersions) {
- String[] cyVersion = cv.getFullVersion().split(versionSplit);
+ String[] cyVersion =
PluginManagerAction.cyVersion.getVersion().split(versionSplit);
String[] plVersion = pluginVersion.split(versionSplit);
if ( PluginVersionUtils.isVersion(pluginVersion,
PluginVersionUtils.MINOR) ) {
cyVersion = new String[]{cyVersion[0], cyVersion[1]};
@@ -527,7 +526,7 @@
+ getCytoscapeVersions().toString() +
"<br>";
Html += "<font color='red'><i>" + toString()
+ " is not verfied to work in the
current version ("
- + CytoscapeVersion.version
+ +
PluginManagerAction.cyVersion.getVersion()
+ ") of Cytoscape.</i></font>";
}
Html += "<p>";
Modified:
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/PluginManager.java
===================================================================
---
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/PluginManager.java
2011-08-23 19:53:34 UTC (rev 26627)
+++
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/PluginManager.java
2011-08-24 00:26:19 UTC (rev 26628)
@@ -69,7 +69,6 @@
import java.util.jar.Manifest;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
-import org.cytoscape.plugin.internal.util.CytoscapeVersion;
/**
* @author skillcoy
@@ -256,10 +255,8 @@
// create plugin manager
private PluginManager(PluginTracker tracker, final
CyApplicationConfiguration config) {
-
- CytoscapeVersion cytoscapeVersion = new CytoscapeVersion();
- cyVersion = cytoscapeVersion.getMajorVersion();
+ cyVersion = new
Integer(PluginManagerAction.cyVersion.getMajorVersion()).toString();
// XXX is this needed anymore?
loadingErrors = new HashSet<Throwable>();
@@ -273,7 +270,7 @@
if (usingWebstartManager()) {
tempDir = new File(config.getSettingLocation(),
"webstart" + File.separator
- + (new
CytoscapeVersion()).getMajorVersion()
+ +
PluginManagerAction.cyVersion.getMajorVersion()
+
File.separator + "plugins");
removeWebstartInstalls();
trackerFileName = "track_webstart_plugins.xml";
Modified:
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/action/PluginManagerAction.java
===================================================================
---
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/action/PluginManagerAction.java
2011-08-23 19:53:34 UTC (rev 26627)
+++
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/action/PluginManagerAction.java
2011-08-24 00:26:19 UTC (rev 26628)
@@ -43,10 +43,12 @@
package org.cytoscape.plugin.internal.action;
import java.awt.event.ActionEvent;
+import java.io.File;
import java.util.List;
import java.util.Map;
import java.util.Properties;
+import org.cytoscape.application.CyApplicationConfiguration;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.CytoscapeVersion;
import org.cytoscape.application.swing.AbstractCyAction;
@@ -82,13 +84,15 @@
public static String cyConfigVerDir;
public static String DefaultPluginUrl = null;
+ public static CytoscapeVersion cyVersion;
/**
* Creates a new BookmarkAction object.
*/
public PluginManagerAction(CySwingApplication desktop,
CyApplicationManager appMgr, CytoscapeVersion version,
CyProperty<Bookmarks> bookmarksProp, BookmarksUtil
bookmarksUtil, GUITaskManager guiTaskManagerServiceRef
- , CyProperty<Properties> cytoscapePropertiesServiceRef,
CyPluginAdapter adapter, TaskFactory pluginLoaderTaskFactory) {
+ , CyProperty<Properties> cytoscapePropertiesServiceRef,
CyPluginAdapter adapter, TaskFactory pluginLoaderTaskFactory,
+ final CyApplicationConfiguration config) {
super("Plugin Manager", appMgr);
@@ -106,9 +110,10 @@
DefaultPluginUrl =
cytoscapePropertiesServiceRef.getProperties().getProperty("defaultPluginDownloadUrl");
// initialize version
- org.cytoscape.plugin.internal.util.CytoscapeVersion.version =
version.getVersion();
- cyConfigVerDir = version.getVersion();
+ cyVersion = version;
+ cyConfigVerDir = new File(config.getSettingLocation(),
File.separator + version.getMajorVersion()).getAbsolutePath();
+
setPreferredMenu("Plugins");
setMenuGravity(1.0f);
Modified:
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/ui/PluginManageDialog.java
===================================================================
---
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/ui/PluginManageDialog.java
2011-08-23 19:53:34 UTC (rev 26627)
+++
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/ui/PluginManageDialog.java
2011-08-24 00:26:19 UTC (rev 26628)
@@ -29,7 +29,7 @@
package org.cytoscape.plugin.internal.ui;
import org.cytoscape.plugin.internal.action.PluginManagerAction;
-import org.cytoscape.plugin.internal.util.CytoscapeVersion;
+
import org.cytoscape.property.CyProperty;
import org.cytoscape.property.bookmark.Bookmarks;
import org.cytoscape.property.bookmark.BookmarksUtil;
@@ -296,7 +296,7 @@
if (NewPlugins.size() <= 0) {
dialog.setError("No plugins compatible
with "
- + new
CytoscapeVersion().getFullVersion()
+ +
PluginManagerAction.cyVersion.getVersion()
+ " available from this
site.");
} else {
dialog.setMessage("");
@@ -1571,15 +1571,15 @@
List<DownloadableInfo> Plugins = new
java.util.ArrayList<DownloadableInfo>();
PluginInfo infoC = new PluginInfo("1", "A Plugin");
- infoC.addCytoscapeVersion(CytoscapeVersion.version);
+
infoC.addCytoscapeVersion(PluginManagerAction.cyVersion.getVersion());
Plugins.add(infoC);
infoC = new PluginInfo("2", "B Plugin");
- infoC.addCytoscapeVersion(CytoscapeVersion.version);
+
infoC.addCytoscapeVersion(PluginManagerAction.cyVersion.getVersion());
Plugins.add(infoC);
infoC = new PluginInfo("3", "C");
- infoC.addCytoscapeVersion(CytoscapeVersion.version);
+
infoC.addCytoscapeVersion(PluginManagerAction.cyVersion.getVersion());
Plugins.add(infoC);
pd.addCategory(Category.NONE.toString(), Plugins,
Modified:
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/ui/PluginUrlDialog.java
===================================================================
---
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/ui/PluginUrlDialog.java
2011-08-23 19:53:34 UTC (rev 26627)
+++
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/ui/PluginUrlDialog.java
2011-08-24 00:26:19 UTC (rev 26628)
@@ -27,6 +27,7 @@
//import org.cytoscape.util.BookmarksUtil;
import org.cytoscape.plugin.internal.CytoscapePlugin;
+import org.cytoscape.plugin.internal.action.PluginManagerAction;
import org.jdesktop.layout.GroupLayout;
import org.jdesktop.layout.LayoutStyle;
import org.slf4j.Logger;
@@ -49,8 +50,8 @@
import javax.swing.JPanel;
import javax.swing.ListCellRenderer;
import javax.swing.WindowConstants;
-import org.cytoscape.plugin.internal.util.CytoscapeVersion;
+
/**
* @author skillcoy
*/
@@ -395,7 +396,7 @@
if (NewPlugins.size() <= 0) {
dialog.setError("No plugins compatible
with "
- + new
CytoscapeVersion().getFullVersion()
+ +
PluginManagerAction.cyVersion.getVersion()
+ " available from this
site.");
} else {
dialog.setMessage("");
Modified:
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/ui/TreeCellRenderer.java
===================================================================
---
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/ui/TreeCellRenderer.java
2011-08-23 19:53:34 UTC (rev 26627)
+++
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/ui/TreeCellRenderer.java
2011-08-24 00:26:19 UTC (rev 26628)
@@ -6,7 +6,7 @@
import javax.swing.tree.DefaultTreeCellRenderer;
import org.cytoscape.plugin.internal.DownloadableInfo;
-import org.cytoscape.plugin.internal.util.CytoscapeVersion;
+import org.cytoscape.plugin.internal.action.PluginManagerAction;
/**
* @author skillcoy
@@ -38,7 +38,7 @@
} else if (leaf && !isOutdated(value)) {
setIcon(okIcon);
setToolTipText("Verified to work in "
- + CytoscapeVersion.version);
+ +
PluginManagerAction.cyVersion.getVersion());
} else {
setToolTipText(null); // no tool tip
}
Deleted:
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/util/CytoscapeVersion.java
===================================================================
---
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/util/CytoscapeVersion.java
2011-08-23 19:53:34 UTC (rev 26627)
+++
core3/impl/trunk/plugin-impl/src/main/java/org/cytoscape/plugin/internal/util/CytoscapeVersion.java
2011-08-24 00:26:19 UTC (rev 26628)
@@ -1,103 +0,0 @@
-/*
- * File: CytoscapeVersion.java Copyright (c) 2006, 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 any later version. This library is
- * distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY,
- * WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR A
- * PARTICULAR PURPOSE. The software and documentation provided hereunder is on
- * an "as is" basis, and the Institute for Systems Biology and the Whitehead
- * Institute have no obligations to provide maintenance, support, updates,
- * enhancements or modifications. In no event shall the Institute for Systems
- * Biology and the Whitehead Institute be liable to any party for direct,
- * indirect, special, incidental or consequential damages, including lost
- * profits, arising out of the use of this software and its documentation, even
- * if the Institute for Systems Biology and the Whitehead Institute have been
- * advised of the possibility of such damage. See the GNU Lesser General Public
- * License for more details. 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.plugin.internal.util;
-
-
-/** CytoscapeVersion: identify (and describe) successive versions of
cytoscape. */
-public class CytoscapeVersion {
- /**
- * This value will be initialized when the bundle get started
- */
- public static String version= null;// = "3.0"; //
=CytoscapeInit.getProperties().getProperty(
- //"cytoscape.version.number");
-
- private static String majorMinorVersion;
-
- private static String bugFixVersion = "0";
-
- /**
- */
- public CytoscapeVersion() {
- //version = props.getProperty("cytoscape.version.number");
- if (version != null){
-
- String[] Versions = version.split("\\.");
- majorMinorVersion = Versions[0] + "." + Versions[1];
-
- if (Versions.length == 3) {
- bugFixVersion = Versions[2];
- }
- }
- }
-
- /**
- * Returns the string 'Cytoscape Version ' and the version number Do
not use
- * to just get a version.
- *
- * @return DOCUMENT ME!
- */
- public String getVersion() {
- return "Cytoscape Version " + version;
- }
-
- /**
- * @return See getVersion()
- */
- public String toString() {
- return getVersion();
- }
-
- /**
- * This method gets the major and minor version for Cytsocape ignoring
- * the bug fix version number. Example: If Cytoscape is currently at
2.4.6
- * this method will return 2.4
- *
- * @return The major and minor version numbers of the currently running
- * Cytoscape.
- */
- public String getMajorVersion() {
- return majorMinorVersion;
- }
-
- /**
- * This method gets the bug fix version for Cytsocape.
- * Example: If Cytoscape is currently at 2.4.6 this method will return 6
- * If there is no bug fix version the default is 0
- *
- * @return Just the bug fix version
- */
- public String getBugFixVersion() {
- return bugFixVersion;
- }
-
- /**
- *
- * @return Full version number for currently running Cytoscape.
- * Ex. 2.4.6
- */
- public String getFullVersion() {
- return version;
- }
-}
Modified:
core3/impl/trunk/plugin-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/impl/trunk/plugin-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-08-23 19:53:34 UTC (rev 26627)
+++
core3/impl/trunk/plugin-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-08-24 00:26:19 UTC (rev 26628)
@@ -140,7 +140,9 @@
<osgi:reference id="bookmarksUtilServiceRef"
interface="org.cytoscape.property.bookmark.BookmarksUtil" />
+ <osgi:reference id="cyApplicationConfigurationServiceRef"
interface="org.cytoscape.application.CyApplicationConfiguration" />
+
<osgi:service id="pluginLoaderTaskFactoryService"
ref="pluginLoaderTaskFactory"
interface="org.cytoscape.work.TaskFactory">
<osgi:service-properties>
Modified:
core3/impl/trunk/plugin-impl/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/impl/trunk/plugin-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-08-23 19:53:34 UTC (rev 26627)
+++
core3/impl/trunk/plugin-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-08-24 00:26:19 UTC (rev 26628)
@@ -67,6 +67,7 @@
<constructor-arg ref="cyPropertyRef" />
<constructor-arg ref="cyPluginAdapter" />
<constructor-arg ref="pluginLoaderTaskFactory" />
+ <constructor-arg ref="cyApplicationConfigurationServiceRef" />
</bean>
<bean id="startupMostlyFinished"
class="org.cytoscape.plugin.internal.StartupMostlyFinished">
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