Author: mes
Date: 2011-01-24 21:15:41 -0800 (Mon, 24 Jan 2011)
New Revision: 23596
Modified:
core3/plugin-impl/trunk/src/main/java/org/cytoscape/plugin/internal/CyPluginAdapterImpl.java
core3/plugin-impl/trunk/src/main/java/org/cytoscape/plugin/internal/PluginManager.java
core3/plugin-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/plugin-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
core3/plugin-impl/trunk/src/test/java/org/cytoscape/plugin/internal/CyPluginAdapterImplTest.java
Log:
added CySwingApplication to api and removed great swaths of unused code
Modified:
core3/plugin-impl/trunk/src/main/java/org/cytoscape/plugin/internal/CyPluginAdapterImpl.java
===================================================================
---
core3/plugin-impl/trunk/src/main/java/org/cytoscape/plugin/internal/CyPluginAdapterImpl.java
2011-01-25 05:15:18 UTC (rev 23595)
+++
core3/plugin-impl/trunk/src/main/java/org/cytoscape/plugin/internal/CyPluginAdapterImpl.java
2011-01-25 05:15:41 UTC (rev 23596)
@@ -14,6 +14,7 @@
import org.cytoscape.model.subnetwork.CyRootNetworkFactory;
import org.cytoscape.session.CyApplicationManager;
import org.cytoscape.session.CySessionManager;
+import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.view.presentation.RenderingEngineFactory;
@@ -40,6 +41,7 @@
private final CyNetworkViewFactory cyNetworkViewFactory;
private final CyRootNetworkFactory cyRootNetworkFactory;
private final CySessionManager cySessionManager;
+ private final CySwingApplication cySwingApplication;
private final RenderingEngineFactory presentationFactory;
private final TaskManager taskManager;
private final VisualMappingManager visualMappingManager;
@@ -60,6 +62,7 @@
CyNetworkViewFactory cyNetworkViewFactory,
CyRootNetworkFactory cyRootNetworkFactory,
CySessionManager cySessionManager,
+ CySwingApplication cySwingApplication,
RenderingEngineFactory presentationFactory,
TaskManager taskManager,
VisualMappingManager visualMappingManager,
@@ -75,6 +78,7 @@
this.cyNetworkViewFactory = cyNetworkViewFactory;
this.cyRootNetworkFactory = cyRootNetworkFactory;
this.cySessionManager = cySessionManager;
+ this.cySwingApplication = cySwingApplication;
this.presentationFactory = presentationFactory;
this.taskManager = taskManager;
this.visualMappingManager = visualMappingManager;
@@ -112,4 +116,6 @@
public CyNetworkViewManager getCyNetworkViewManager() { return
networkViewManager; }
public CyApplicationManager getCyApplicationManager() { return
applicationManager; }
+
+ public CySwingApplication getCySwingApplication() { return
cySwingApplication; }
}
Modified:
core3/plugin-impl/trunk/src/main/java/org/cytoscape/plugin/internal/PluginManager.java
===================================================================
---
core3/plugin-impl/trunk/src/main/java/org/cytoscape/plugin/internal/PluginManager.java
2011-01-25 05:15:18 UTC (rev 23595)
+++
core3/plugin-impl/trunk/src/main/java/org/cytoscape/plugin/internal/PluginManager.java
2011-01-25 05:15:41 UTC (rev 23596)
@@ -284,9 +284,7 @@
logger.info("Creating directories for "
+ tempDir.getAbsolutePath());
if (!tempDir.mkdirs()) {
-
- System.out.println("Failed to create directory
--- "+ tempDir.getAbsolutePath());
- //Cytoscape.exit(-1);
+ logger.warn("Failed to create directory --- "+
tempDir.getAbsolutePath());
}
}
@@ -711,7 +709,6 @@
}
// don't need to register if we have the info object
InstallablePlugin insp = new InstallablePlugin(p);
- //loadURLPlugins(ToLoad, false);
if (duplicateLoadError) {
insp.uninstall();
@@ -721,108 +718,6 @@
}
- /**
- * Parses the plugin input strings and transforms them into the
appropriate
- * URLs or resource names. The method first checks to see if the
- */
- public void loadPlugins(List<String> p) {
-
- Set<String> PluginsSeen = new HashSet<String>();
-
- // Parse the plugin strings and determine whether they're urls,
- // files, directories, class names, or manifest file names.
- for (String currentPlugin : p) {
- try {
- if (PluginsSeen.contains(currentPlugin))
- continue;
-
- if (currentPlugin.contains(".cytoscape")) {
- logger.info(currentPlugin);
- }
-
- File f = new File(currentPlugin);
-
- // If the file name ends with .jar add it to
the list as a url.
- if (currentPlugin.endsWith(".jar")) {
- PluginsSeen.add(f.getAbsolutePath());
-
- // If the name doesn't match a url,
turn it into one.
- if
(!currentPlugin.matches(FileUtil.urlPattern)) {
- logger.info(" - file: " +
f.getAbsolutePath());
-
pluginURLs.add(jarURL(f.getAbsolutePath()));
- } else {
- logger.info(" - url: " +
f.getAbsolutePath());
-
pluginURLs.add(jarURL(currentPlugin));
- }
- } else if (!f.exists()) {
- // If the file doesn't exists, assume
- // that it's a resource plugin.
- logger.info(" - classpath: " +
currentPlugin);
- resourcePlugins.add(currentPlugin);
- } else if (f.isDirectory()) {
- // If the file is a directory, load
- // all of the jars in the directory.
- logger.info(" - directory: " +
f.getAbsolutePath());
-
- for (String fileName : f.list()) {
- if (!fileName.endsWith(".jar"))
{
- continue;
- }
-
PluginsSeen.add(f.getAbsolutePath()
- +
System.getProperty("file.separator")
- + fileName);
-
pluginURLs.add(jarURL(f.getAbsolutePath()
- +
System.getProperty("file.separator")
- + fileName));
- }
- } else {
- // Assume the file is a manifest (i.e.
list of jar names)
- // and make urls out of them.
- logger.info(" - file manifest: "
- + f.getAbsolutePath());
-
- String text =
FileUtil.getInputString(currentPlugin);
-
- String[] allLines = text.split(System
-
.getProperty("line.separator"));
- for (String pluginLoc : allLines) {
- if (pluginLoc.endsWith(".jar"))
{
-
PluginsSeen.add(pluginLoc);
- if
(pluginLoc.matches(FileUtil.urlPattern)) {
-
pluginURLs.add(jarURL(pluginLoc));
- } else {
- // TODO this
should have a better error
- // perhaps,
throw an exception??
-
logger.warn("Plugin location specified in "
-
+ currentPlugin
-
+ " is not a valid url: "
-
+ pluginLoc
-
+ " -- NOT adding it.");
-
loadingErrors.add(new PluginException(
-
"Plugin location specified in "
-
+ currentPlugin
-
+ " is not a valid url: "
-
+ pluginLoc
-
+ " -- NOT adding it."));
- }
- }
- }
- }
- // Catching Throwable because Errors (e.g.
NoClassDefFoundError) could
- // cause Cytoscape to crash, which plugins should
definitely not do.
- } catch (Throwable t) {
- loadingErrors.add(new PluginException("problem
loading plugin: "+currentPlugin,t));
- }
- }
- // now load the plugins in the appropriate manner
- loadURLPlugins(pluginURLs, true);
- loadResourcePlugins(resourcePlugins);
-
- cleanCurrentList();
- if (duplicateLoadError)
- addDuplicateError();
- }
-
private void addDuplicateError() {
String Msg = "The following plugins were not loaded due to
duplicate class definitions:\n";
for (String dup : duplicateClasses)
@@ -831,203 +726,6 @@
loadingErrors.add(new DuplicatePluginClassException(Msg));
}
- /**
- * Load all plugins by using the given URLs loading them all on one
- * URLClassLoader, then interating through each Jar file looking for
classes
- * that are CytoscapePlugins
- */
- private void loadURLPlugins(List<URL> pluginUrls, boolean register) {
-
-
- System.out.println("\nPluginManager.loadURLPlugins()....\n");
-
-
- URL[] urls = new URL[pluginUrls.size()];
- pluginUrls.toArray(urls);
-
- duplicateClasses = new ArrayList<String>();
- duplicateLoadError = false;
-
- for (URL url : urls) {
- try {
- addClassPath(url);
- // Catching Throwable because Errors (e.g.
NoClassDefFoundError) could
- // cause Cytoscape to crash, which plugins should
definitely not do.
- } catch (Throwable t) {
- loadingErrors.add(new
PluginException("Classloader Error: " + url, t));
- }
- }
-
- // the creation of the class loader automatically loads the
plugins
- classLoader = (URLClassLoader)
ClassLoader.getSystemClassLoader();
-
- // iterate through the given jar files and find classes that are
- // assignable from CytoscapePlugin
- for (int i = 0; i < urls.length; ++i) {
-
- }
-
- /*
- try {
- logger.info("attempting to load plugin url:
"+urls[i]);
-
- JarURLConnection jc = (JarURLConnection) urls[i]
- .openConnection();
- // Ensure we are reading the real content from
urls[i],
- // and not some out-of-date cached content:
- jc.setUseCaches(false);
- JarFile jar = jc.getJarFile();
-
- // if the jar file is null, do nothing
- if (jar == null) {
- continue;
- }
-
- // try to get class name from the manifest file
- String className =
JarUtil.getPluginClass(jar.getName(),
- PluginInfo.FileType.JAR);
-
- if (className != null) {
- Class pc = getPluginClass(className);
-
- if (pc != null) {
- logger.info("Loading from
manifest");
- loadPlugin(pc, jar, register);
- continue;
- }
- }
-
- // new-school failed, so revert to old school.
Search through
- // the jar entries
- Enumeration entries = jar.entries();
-
- if (entries == null) {
- loadingErrors.add(new
PluginException("Jar file "
- + jar.getName()
- + " has no entries,
skipped loading."));
- logger.warn("Jar file "
- + jar.getName()
- + " has no entries,
skipped loading.");
- continue;
- }
-
- int totalPlugins = 0;
- while (entries.hasMoreElements()) {
- // get the entry
- String entry =
entries.nextElement().toString();
-
- if (entry.endsWith("class")) {
- // convert the entry to an
assignable class name
- entry =
entry.replaceAll("\\.class$", "");
- // A regex to match the two
known types of file
- // separators. We can't use
File.separator because
- // the system the jar was
created on is not
- // necessarily the same is the
one it is running on.
- entry =
entry.replaceAll("/|\\\\", ".");
-
- Class pc =
getPluginClass(entry);
- if (pc == null) {
- continue;
- }
- totalPlugins++;
- loadPlugin(pc, jar, register);
- break;
- }
- }
- if (totalPlugins == 0) {
- logger.info("No plugin found in
specified jar - assuming it's a library.");
- }
- // Catching Throwable because Errors (e.g.
NoClassDefFoundError) could
- // cause Cytoscape to crash, which plugins should
definitely not do.
- } catch (Throwable t) {
- loadingErrors.add(new PluginException("problem
loading plugin URL: " + urls[i], t));
- }
- }
- */
- }
-
- // these are jars that *may or may not* extend CytoscapePlugin but may
be
- // used by jars that do
- private void loadResourcePlugins(List<String> resourcePlugins) {
- // attempt to load resource plugins
- for (String resource : resourcePlugins) {
- logger.info("attempting to load plugin resourse: " +
resource);
-
- // try to get the class
- try {
- Class rclass = Class.forName(resource);
- loadPlugin(rclass, null, true);
- // Catching Throwable because Errors (e.g.
NoClassDefFoundError) could
- // cause Cytoscape to crash, which plugins should
definitely not do.
- } catch (Throwable t) {
- loadingErrors.add(new PluginException("problem
loading plugin resource: " + resource, t));
- }
- }
- }
-
- private void loadPlugin(Class plugin, JarFile jar, boolean register)
- throws PluginException {
- if (CytoscapePlugin.class.isAssignableFrom(plugin)
- && !loadedPlugins.contains(plugin.getName())) {
-
- Object obj = CytoscapePlugin.loadPlugin(plugin);
- if (obj != null) {
- loadedPlugins.add(plugin.getName());
- if (register) {
- register((CytoscapePlugin) obj, jar);
- }
- }
-
- } else if (loadedPlugins.contains(plugin.getName())) {
- duplicateClasses.add(plugin.getName());
- duplicateLoadError = true;
- }
- }
-
- /**
- * Determines whether the class with a particular name extends
- * CytoscapePlugin by attempting to load the class first.
- *
- * @param name
- * the name of the putative plugin class
- */
- private Class getPluginClass(String name) throws ClassNotFoundException,
- NoClassDefFoundError {
- Class c = classLoader.loadClass(name);
- if (CytoscapePlugin.class.isAssignableFrom(c))
- return c;
- else
- return null;
- }
-
- // creates a URL object from a jar file name
- private static URL jarURL(String urlString) throws
MalformedURLException {
- String uString;
- if (urlString.matches(FileUtil.urlPattern)) {
- uString = "jar:" + urlString + "!/";
- } else {
- uString = "jar:file:" + urlString + "!/";
- }
- return new URL(uString);
- }
-
- /**
- * This will be used to add plugin jars' URL to the System Loader's
- * classpath.
- *
- * @param url
- * @throws NoSuchMethodException
- * @throws IllegalAccessException
- * @throws InvocationTargetException
- */
- private void addClassPath(URL url) throws NoSuchMethodException,
- IllegalAccessException, InvocationTargetException {
- Method method = URLClassLoader.class.getDeclaredMethod("addURL",
- new Class[] { URL.class });
- method.setAccessible(true);
- method.invoke(ClassLoader.getSystemClassLoader(), new Object[]
{ url });
- }
-
public void setCyPluginAdapter(CyPluginAdapter adapter){
this.adapter = adapter;
Modified:
core3/plugin-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/plugin-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-01-25 05:15:18 UTC (rev 23595)
+++
core3/plugin-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-01-25 05:15:41 UTC (rev 23596)
@@ -52,6 +52,10 @@
interface="org.cytoscape.session.CySessionManager">
</osgi:reference>
+ <osgi:reference id="cySwingApplicationRef"
+ interface="org.cytoscape.application.swing.CySwingApplication">
+ </osgi:reference>
+
<osgi:reference id="presentationFactoryRef"
interface="org.cytoscape.view.presentation.RenderingEngineFactory">
</osgi:reference>
Modified:
core3/plugin-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/plugin-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-01-25 05:15:18 UTC (rev 23595)
+++
core3/plugin-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-01-25 05:15:41 UTC (rev 23596)
@@ -29,6 +29,7 @@
<constructor-arg ref="cyNetworkViewFactoryRef" />
<constructor-arg ref="cyRootNetworkFactoryRef" />
<constructor-arg ref="cySessionManagerRef" />
+ <constructor-arg ref="cySwingApplicationRef" />
<constructor-arg ref="presentationFactoryRef" />
<constructor-arg ref="taskManagerRef" />
<constructor-arg ref="visualMappingManagerRef" />
Modified:
core3/plugin-impl/trunk/src/test/java/org/cytoscape/plugin/internal/CyPluginAdapterImplTest.java
===================================================================
---
core3/plugin-impl/trunk/src/test/java/org/cytoscape/plugin/internal/CyPluginAdapterImplTest.java
2011-01-25 05:15:18 UTC (rev 23595)
+++
core3/plugin-impl/trunk/src/test/java/org/cytoscape/plugin/internal/CyPluginAdapterImplTest.java
2011-01-25 05:15:41 UTC (rev 23596)
@@ -7,6 +7,7 @@
import org.cytoscape.model.subnetwork.CyRootNetworkFactory;
import org.cytoscape.session.CyApplicationManager;
import org.cytoscape.session.CySessionManager;
+import org.cytoscape.application.swing.CySwingApplication;
//import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -31,6 +32,7 @@
CyNetworkViewFactory cyNetworkViewFactory =
mock(CyNetworkViewFactory.class);
CyRootNetworkFactory cyRootNetworkFactory =
mock(CyRootNetworkFactory.class);
CySessionManager cySessionManager =
mock(CySessionManager.class);
+ CySwingApplication cySwingApplication =
mock(CySwingApplication.class);
RenderingEngineFactory presentationFactory =
mock(RenderingEngineFactory.class);
TaskManager taskManager = mock(TaskManager.class);
VisualMappingManager visualMappingManager =
mock(VisualMappingManager.class);
@@ -46,6 +48,7 @@
cyNetworkViewFactory,
cyRootNetworkFactory,
cySessionManager,
+ cySwingApplication,
presentationFactory,
taskManager,
visualMappingManager,
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