version 3.0.0-M5-SNAPSHOT with 3.0.0-beta2-SNAPSHOT APIs

[Michael Heuer]

Hello,

I need to use the 3.0.0-beta2-SNAPSHOT APIs.

When I check out app-developer/trunk, the pom is using 3.0.0-beta1 for
the parent pom and API version. I tried building 3.0.0-M5-SNAPSHOT
after updating app-developer/trunk/pom.xml to use 3.0.0-beta2-SNAPSHOT
for the API version.

$ svn diff .
Index: pom.xml
===================================================================
--- pom.xml (revision 29679)
+++ pom.xml (working copy)
@@ -4,7 +4,7 @@
<parent>
<groupId>org.cytoscape</groupId>
<artifactId>parent</artifactId>
- <version>3.0.0-beta1</version>
+ <version>3.0.0-beta2-SNAPSHOT</version>
<relativePath>../parent</relativePath>
</parent>

@@ -14,7 +14,7 @@
<version>3.0.0-M5-SNAPSHOT</version>

<properties>
- <cytoscape.api.version>3.0.0-beta1</cytoscape.api.version>
+ <cytoscape.api.version>3.0.0-beta2-SNAPSHOT</cytoscape.api.version>
<cytoscape.distribution.version>${project.version}</cytoscape.distribution.version>
</properties>


It builds ok but at runtime I get a bunch of class not found
exceptions, including this one when trying to create a new empty
network:

pool-10-thread-2 WARN
[org.cytoscape.work.internal.task.JDialogTaskManager] - Caught
exception executing task.
java.lang.NoClassDefFoundError: org/cytoscape/model/events/NetworkAddedEvent
at org.cytoscape.model.internal.CyNetworkManagerImpl.addNetwork(CyNetworkManagerImpl.java:130)
at org.cytoscape.task.internal.creation.NewEmptyNetworkTask.run(NewEmptyNetworkTask.java:81)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskThread.run(JDialogTaskManager.java:220)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:679)
Caused by: java.lang.ClassNotFoundException:
org.cytoscape.model.events.NetworkAddedEvent not found by
org.cytoscape.model-impl [121]
at org.apache.felix.framework.ModuleImpl.findClassOrResourceByDelegation(ModuleImpl.java:787)
at org.apache.felix.framework.ModuleImpl.access$400(ModuleImpl.java:71)
at org.apache.felix.framework.ModuleImpl$ModuleClassLoader.loadClass(ModuleImpl.java:1768)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
... 9 more


michael

[Mike Smoot]

I'm not sure what's going on.  Are you also using the nightly build (i.e. this) to run your app?  If that's not it, could you send me the app offline so that I can debug?

thanks,

Mike

  michael

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____________________________________________________________
Michael Smoot, Ph.D.              
UCSD Department of Medicine
tel: 858-822-4756

[Michael Heuer]

Hello Mike,

With app-developer/trunk and no modifications it downloads this snapshot

Downloaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/distribution/cytoscape/3.0.0-M5-SNAPSHOT/cytoscape-3.0.0-M5-20120625.020209-147.tar.gz
(64214 KB at 344.6 KB/sec)

and Cytoscape loads and runs fine. Create new empty network works ok.


If I install my app which depends on 3.0.0-beta2 APIs to
framework/deploy and restart, I get a bunch of exceptions at startup

$ ./cytoscape.sh
_
___ _ _| |_ ___ ___ ___ __ _ _ __ ___
/ __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \
| (__| |_| | |_| (_) \__ \ (__| (_| | |_) | __/
\___|\__, |\__|\___/|___/\___|\__,_| .__/ \___|
|___/ |_|

Cytoscape 3.0.0-M5-SNAPSHOT

Hit '<tab>' for a list of available commands
and '[cmd] --help' for help on a specific command.
Hit '<ctrl-d>' or 'osgi:shutdown' to shutdown Cytoscape.

Cytoscape 3.0.0-M5-SNAPSHOT> Should not skip: ^
Should not skip: ^
Should not skip: ^
Should not skip: ^
Should not skip: ^
Should not skip: ^
Should not skip: ^
Should not skip: ^
Should not skip: ^

Thread-11 WARN [org.ops4j.pax.swissbox.bnd.BndUtils] - Bundle cannot
be generated
ERROR: Bundle org.cytoscape.vizmap-gui-impl [142] Error starting
mvn:org.cytoscape/vizmap-gui-impl/3.0.0-alpha9-SNAPSHOT
(org.osgi.framework.BundleException: Activator start error in bundle
org.cytoscape.vizmap-gui-impl [142].)
java.lang.NoClassDefFoundError: org/cytoscape/model/subnetwork/CyRootNetwork
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at org.apache.felix.framework.ModuleImpl$ModuleClassLoader.findClass(ModuleImpl.java:1907)
at org.apache.felix.framework.ModuleImpl.findClassOrResourceByDelegation(ModuleImpl.java:727)

at org.apache.felix.framework.ModuleImpl.access$400(ModuleImpl.java:71)
at org.apache.felix.framework.ModuleImpl$ModuleClassLoader.loadClass(ModuleImpl.java:1768)

at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at org.cytoscape.model.internal.CyNetworkFactoryImpl.createNetworkWithPrivateTables(CyNetworkFactoryImpl.java:96)
at org.cytoscape.view.vizmap.gui.internal.DefaultViewPanelImpl.<init>(DefaultViewPanelImpl.java:115)
at org.cytoscape.view.vizmap.gui.internal.CyActivator.start(CyActivator.java:120)
at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:629)
at org.apache.felix.framework.Felix.activateBundle(Felix.java:1842)
at org.apache.felix.framework.Felix.startBundle(Felix.java:1759)
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1163)
at org.apache.felix.framework.StartLevelImpl.run(StartLevelImpl.java:264)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.ClassNotFoundException:
org.cytoscape.model.subnetwork.CyRootNetwork not found by

org.cytoscape.model-impl [121]
at org.apache.felix.framework.ModuleImpl.findClassOrResourceByDelegation(ModuleImpl.java:787)
at org.apache.felix.framework.ModuleImpl.access$400(ModuleImpl.java:71)
at org.apache.felix.framework.ModuleImpl$ModuleClassLoader.loadClass(ModuleImpl.java:1768)

at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
... 17 more
_
___ _ _| |_ ___ ___ ___ __ _ _ __ ___
/ __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \
| (__| |_| | |_| (_) \__ \ (__| (_| | |_) | __/
\___|\__, |\__|\___/|___/\___|\__,_| .__/ \___|
|___/ |_|

Cytoscape 3.0.0-M5-SNAPSHOT

Hit '<tab>' for a list of available commands
and '[cmd] --help' for help on a specific command.
Hit '<ctrl-d>' or 'osgi:shutdown' to shutdown Cytoscape.

Cytoscape 3.0.0-M5-SNAPSHOT> ERROR: Bundle org.cytoscape.psi-mi-impl
[151] Error starting
mvn:org.cytoscape/psi-mi-impl/3.0.0-alpha9-SNAPSHOT
(org.osgi.framework.BundleException: Activator start error in bundle
org.cytoscape.psi-mi-impl [151].)
java.lang.RuntimeException: Couldn't find service:
org.cytoscape.io.util.StreamUtil
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:44)
at org.cytoscape.service.util.AbstractCyActivator.getService(AbstractCyActivator.java:93)
at org.cytoscape.psi_mi.internal.CyActivator.start(CyActivator.java:36)
at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:629)
at org.apache.felix.framework.Felix.activateBundle(Felix.java:1842)
at org.apache.felix.framework.Felix.startBundle(Felix.java:1759)
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1163)
at org.apache.felix.framework.StartLevelImpl.run(StartLevelImpl.java:264)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NullPointerException: ServiceReference is null
for: org.cytoscape.io.util.StreamUtil
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:38)
... 8 more
ERROR: Bundle org.cytoscape.network-analyzer-impl [152] Error starting
mvn:org.cytoscape/network-analyzer-impl/3.0.0-alpha9-SNAPSHOT
(org.osgi.framework.BundleException: Activator start error in bundle
org.cytoscape.network-analyzer-impl [152].)
java.lang.RuntimeException: Couldn't find service:
org.cytoscape.io.read.CyNetworkReaderManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:44)
at org.cytoscape.service.util.AbstractCyActivator.getService(AbstractCyActivator.java:93)
at de.mpg.mpi_inf.bioinf.netanalyzer.CyActivator.start(CyActivator.java:48)
at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:629)
at org.apache.felix.framework.Felix.activateBundle(Felix.java:1842)
at org.apache.felix.framework.Felix.startBundle(Felix.java:1759)
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1163)
at org.apache.felix.framework.StartLevelImpl.run(StartLevelImpl.java:264)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NullPointerException: ServiceReference is null
for: org.cytoscape.io.read.CyNetworkReaderManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:38)
... 8 more
ERROR: Bundle org.cytoscape.table-import-impl [153] Error starting
mvn:org.cytoscape/table-import-impl/3.0.0-alpha9-SNAPSHOT
(org.osgi.framework.BundleException: Activator start error in bundle
org.cytoscape.table-import-impl [153].)
java.lang.RuntimeException: Couldn't find service:
org.cytoscape.io.util.StreamUtil
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:44)
at org.cytoscape.service.util.AbstractCyActivator.getService(AbstractCyActivator.java:93)
at org.cytoscape.tableimport.internal.CyActivator.start(CyActivator.java:77)
at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:629)
at org.apache.felix.framework.Felix.activateBundle(Felix.java:1842)
at org.apache.felix.framework.Felix.startBundle(Felix.java:1759)
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1163)
at org.apache.felix.framework.StartLevelImpl.run(StartLevelImpl.java:264)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NullPointerException: ServiceReference is null
for: org.cytoscape.io.util.StreamUtil
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:38)
... 8 more
ERROR: Bundle org.cytoscape.sbml-impl [157] Error starting
mvn:org.cytoscape/sbml-impl/3.0.0-alpha9-SNAPSHOT
(org.osgi.framework.BundleException: Activator start error in bundle
org.cytoscape.sbml-impl [157].)
java.lang.RuntimeException: Couldn't find service:
org.cytoscape.io.util.StreamUtil
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:44)
at org.cytoscape.service.util.AbstractCyActivator.getService(AbstractCyActivator.java:93)
at org.cytoscape.sbml.internal.CyActivator.start(CyActivator.java:31)
at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:629)
at org.apache.felix.framework.Felix.activateBundle(Felix.java:1842)
at org.apache.felix.framework.Felix.startBundle(Felix.java:1759)
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1163)
at org.apache.felix.framework.StartLevelImpl.run(StartLevelImpl.java:264)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NullPointerException: ServiceReference is null
for: org.cytoscape.io.util.StreamUtil
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:38)
... 8 more
ERROR: Bundle org.cytoscape.cpath2-impl [158] Error starting
mvn:org.cytoscape/cpath2-impl/3.0.0-alpha9-SNAPSHOT
(org.osgi.framework.BundleException: Activator start error in bundle
org.cytoscape.cpath2-impl [158].)
java.lang.RuntimeException: Couldn't find service:
org.cytoscape.io.read.CyNetworkReaderManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:44)
at org.cytoscape.service.util.AbstractCyActivator.getService(AbstractCyActivator.java:93)
at org.cytoscape.cpath2.internal.CyActivator.start(CyActivator.java:47)
at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:629)
at org.apache.felix.framework.Felix.activateBundle(Felix.java:1842)
at org.apache.felix.framework.Felix.startBundle(Felix.java:1759)
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1163)
at org.apache.felix.framework.StartLevelImpl.run(StartLevelImpl.java:264)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NullPointerException: ServiceReference is null
for: org.cytoscape.io.read.CyNetworkReaderManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:38)
... 8 more
ERROR: Bundle org.cytoscape.graphml-impl [160] Error starting
mvn:org.cytoscape/graphml-impl/3.0.0-alpha9-SNAPSHOT
(org.osgi.framework.BundleException: Activator start error in bundle
org.cytoscape.graphml-impl [160].)
java.lang.RuntimeException: Couldn't find service:
org.cytoscape.io.util.StreamUtil
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:44)
at org.cytoscape.service.util.AbstractCyActivator.getService(AbstractCyActivator.java:93)
at org.cytoscape.io.internal.CyActivator.start(CyActivator.java:28)
at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:629)
at org.apache.felix.framework.Felix.activateBundle(Felix.java:1842)
at org.apache.felix.framework.Felix.startBundle(Felix.java:1759)
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1163)
at org.apache.felix.framework.StartLevelImpl.run(StartLevelImpl.java:264)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NullPointerException: ServiceReference is null
for: org.cytoscape.io.util.StreamUtil
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:38)
... 8 more
ERROR: Bundle org.cytoscape.app-impl [163] Error starting
mvn:org.cytoscape/app-impl/3.0.0-alpha9-SNAPSHOT
(org.osgi.framework.BundleException: Activator start error in bundle
org.cytoscape.app-impl [163].)
java.lang.RuntimeException: Couldn't find service:
org.cytoscape.io.read.CyNetworkReaderManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:44)
at org.cytoscape.service.util.AbstractCyActivator.getService(AbstractCyActivator.java:93)
at org.cytoscape.app.internal.CyActivator.start(CyActivator.java:144)
at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:629)
at org.apache.felix.framework.Felix.activateBundle(Felix.java:1842)
at org.apache.felix.framework.Felix.startBundle(Felix.java:1759)
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1163)
at org.apache.felix.framework.StartLevelImpl.run(StartLevelImpl.java:264)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NullPointerException: ServiceReference is null
for: org.cytoscape.io.read.CyNetworkReaderManager
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:38)
... 8 more
ERROR: Bundle org.cytoscape.scripting-impl [164] Error starting
mvn:org.cytoscape/scripting-impl/3.0.0-alpha9-SNAPSHOT
(org.osgi.framework.BundleException: Activator start error in bundle
org.cytoscape.scripting-impl [164].)
java.lang.RuntimeException: Couldn't find service:
org.cytoscape.app.CyAppAdapter
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:44)
at org.cytoscape.service.util.AbstractCyActivator.getService(AbstractCyActivator.java:93)
at org.cytoscape.scripting.internal.CyActivator.start(CyActivator.java:15)
at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:629)
at org.apache.felix.framework.Felix.activateBundle(Felix.java:1842)
at org.apache.felix.framework.Felix.startBundle(Felix.java:1759)
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1163)
at org.apache.felix.framework.StartLevelImpl.run(StartLevelImpl.java:264)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NullPointerException: ServiceReference is null
for: org.cytoscape.app.CyAppAdapter
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:38)
... 8 more
ERROR: Bundle org.cytoscape.gui-cmdline-parser-impl [165] Error
starting mvn:org.cytoscape/gui-cmdline-parser-impl/3.0.0-alpha9-SNAPSHOT
(org.osgi.framework.BundleException: Activator start error in bundle
org.cytoscape.gui-cmdline-parser-impl [165].)
java.lang.RuntimeException: Couldn't find service:
org.cytoscape.io.util.StreamUtil
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:44)
at org.cytoscape.service.util.AbstractCyActivator.getService(AbstractCyActivator.java:93)
at org.cytoscape.cmdline.gui.internal.CyActivator.start(CyActivator.java:29)
at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:629)
at org.apache.felix.framework.Felix.activateBundle(Felix.java:1842)
at org.apache.felix.framework.Felix.startBundle(Felix.java:1759)
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1163)
at org.apache.felix.framework.StartLevelImpl.run(StartLevelImpl.java:264)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NullPointerException: ServiceReference is null
for: org.cytoscape.io.util.StreamUtil
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:38)
... 8 more
ERROR: Bundle org.cytoscape.welcome-impl [166] Error starting
mvn:org.cytoscape/welcome-impl/3.0.0-alpha9-SNAPSHOT
(org.osgi.framework.BundleException: Activator start error in bundle
org.cytoscape.welcome-impl [166].)
java.lang.RuntimeException: Couldn't find service:
org.cytoscape.io.util.RecentlyOpenedTracker
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:44)
at org.cytoscape.service.util.AbstractCyActivator.getService(AbstractCyActivator.java:93)
at org.cytoscape.welcome.internal.CyActivator.start(CyActivator.java:26)
at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:629)
at org.apache.felix.framework.Felix.activateBundle(Felix.java:1842)
at org.apache.felix.framework.Felix.startBundle(Felix.java:1759)
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1163)
at org.apache.felix.framework.StartLevelImpl.run(StartLevelImpl.java:264)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NullPointerException: ServiceReference is null
for: org.cytoscape.io.util.RecentlyOpenedTracker
at org.cytoscape.service.util.internal.utils.ServiceUtil.getService(ServiceUtil.java:38)
... 8 more


Then I maven clean, apply the patch below to pom.xml to use
3.0.0-beta2-SNAPSHOT APIs, and rebuild. Cytoscape loads and runs
fine. Create new empty network works ok.


Only after I install my app to framework/deploy and restart does the
issue arise. File --> New --> Network --> Empty Network. In this
build I get an error dialog box:

The task could not be completed because an error has occurred.
java.lang.NoClassDefFoundError: org/cytoscape/model/events/NetworkAddedEvent

java.lang.Exception: java.lang.NoClassDefFoundError:
org/cytoscape/model/events/NetworkAddedEvent
org.cytoscape.work.internal.task.JDialogTaskManager$TaskThread.run(JDialogTaskManager.java:248)
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
java.util.concurrent.FutureTask.run(FutureTask.java:138)
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
java.lang.Thread.run(Thread.java:680)
java.lang.NoClassDefFoundError: org/cytoscape/model/events/NetworkAddedEvent
org.cytoscape.model.internal.CyNetworkManagerImpl.addNetwork(CyNetworkManagerImpl.java:130)
org.cytoscape.task.internal.creation.NewEmptyNetworkTask.run(NewEmptyNetworkTask.java:81)
org.cytoscape.work.internal.task.JDialogTaskManager$TaskThread.run(JDialogTaskManager.java:220)
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
java.util.concurrent.FutureTask.run(FutureTask.java:138)
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
java.lang.Thread.run(Thread.java:680)

java.lang.ClassNotFoundException:
org.cytoscape.model.events.NetworkAddedEvent not found by
org.cytoscape.model-impl [121]

org.apache.felix.framework.ModuleImpl.findClassOrResourceByDelegation(ModuleImpl.java:787)
org.apache.felix.framework.ModuleImpl.access$400(ModuleImpl.java:71)
org.apache.felix.framework.ModuleImpl$ModuleClassLoader.loadClass(ModuleImpl.java:1768)
java.lang.ClassLoader.loadClass(ClassLoader.java:247)
org.cytoscape.model.internal.CyNetworkManagerImpl.addNetwork(CyNetworkManagerImpl.java:130)
org.cytoscape.task.internal.creation.NewEmptyNetworkTask.run(NewEmptyNetworkTask.java:81)
org.cytoscape.work.internal.task.JDialogTaskManager$TaskThread.run(JDialogTaskManager.java:220)
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
java.util.concurrent.FutureTask.run(FutureTask.java:138)
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
java.lang.Thread.run(Thread.java:680)


The app does not use NetworkAddedEvent directly. It registers group
listeners via CyServiceRegistrar:

Properties properties = new Properties();
serviceRegistrar.registerService(this,
GroupAboutToBeDestroyedListener.class, properties);
serviceRegistrar.registerService(this,
GroupAboutToBeRemovedListener.class, properties);
serviceRegistrar.registerService(this, GroupAddedListener.class,
properties);
serviceRegistrar.registerService(this,
GroupAddedToNetworkListener.class, properties);

michael